Method for Production and Use of Mite Group 1 Proteins

ABSTRACT

The present invention includes a method to produce a recombinant mite Group 1 protein in a methyltrophic yeast or an  Escherichia coli  microorganism. The present invention also relates to a recombinant mite Group 1 protein obtained by such a method, such a recombinant protein being able to selectively bind IgE or cause proliferation of a T cell that proliferates in response to a native mite Group 1 protein. Also included in the present invention is the use of such a recombinant mite Group 1 protein to detect mite allergy or to reduce an allergic response to a mite Group 1 protein. The present invention also includes novel mite Group 1 nucleic acid molecules, proteins, recombinant molecules, and recombinant cells, as well as uses thereof.

This application claims priority to U.S. Provisional Patent ApplicationSer. No. 60/159,841, filed Oct. 15, 1999

FIELD OF THE INVENTION

The present invention relates to a method of expressing an activerecombinant mite Group 1 protein in a methyltrophic yeast microorganismor in Escherichia coli. The present invention also relates to use ofsuch a protein to detect mite allergy or to reduce an allergic response.

BACKGROUND OF THE INVENTION

The cross-linking of mast cell-bound IgE upon binding of IgE toallergens induces Type I allergic diseases such as atopic dermatitis andatopic asthma. Diseases related to allergy and atopy affect asignificant percentage of the population, including up to 20% of humans,and are increasing every year. A significant proportion of type Iallergic patients are mite allergic. For example, based on skin tests,at least 75% of the estimated 50 million asthmatics in the United Statesare mite allergic. As such, mite proteins comprise an important allergenin type I allergic disease. The house dust mites Dermatophagoidesfarinae and Dermatophagoides pteronyssinus are the most common mites inthe United States. These mites produce several classes, or groups, ofallergens, one of which is known as Group 1 proteins, which are alsofound in other mite species. For example, considerable cross-reactivityhas been found among Blomia tropicalis, D. farinae and Lepidoglyphusdestructor allergens; see, for example, Colloff, 1993, J Allergy ClinImmunol 91, 1042-1050. Additionally, Group 1 proteins have been found inD. pteronyssinus, D. farinae, Euroglyphus maynei, and L. destructor;see, for example, Thomas et al, 1998, Allergy 53, 821-832.

Mite Group 1 proteins share significant homology with a family ofcysteine proteases including actinidin, papain, cathepsin H andcathepsin B. These Group 1 proteins are commonly found in the feces ofmites and are thought to function as digestive enzymes in the miteintestine. Group 1 proteins from different mites are highly homologous,approximately 25-kilodalton (kD) secretory glycoproteins, that aresynthesized by the cell as a pre-pro-protein that is processed to amature form. D. farinae, D. pteronyssinus, and E. maynei Group 1proteins, for example, share about 80% identity. In particular, Group 1proteins from D. farinae and D. pteronyssinus, also referred to as Der f1 and Der p 1 proteins, respectively, show extensive cross-reactivity inbinding IgE and IgG. In human populations that are mite allergic,approximately 80% to 90% have IgE that is reactive to Group 1 proteins;see Thomas, 1996, Adv Exp Med Biol 409, 85-93.

Since Group 1 proteins are important in mite allergy, it is desirable tohave sufficient quantities of these proteins for uses related todiagnosing and treating diseases that are related to mite allergy. Toobtain the amounts of Group 1 proteins necessary for these purposes, itis desirable to use recombinant expression systems, since the amount ofGroup 1 proteins in mites is relatively small and the purificationprocess to obtain native Group 1 proteins is a difficult, multi-stepprocess. Nucleic acid molecules encoding Der f 1 and Der p 1 proteinswere isolated a number of years (see, for example, U.S. Pat. No.5,433,948, issued Jul. 18, 1995, by Thomas et al; U.S. Pat. No.5,552,142, issued Sep. 3, 1996, by Thomas et al; U.S. Pat. No.5,770,202, issued Jun. 23, 1998, by Thomas et al; U.S. Pat. No.5,773,002, issued Jun. 30, 1998, by Thomas et al; PCT Patent PublicationNo. WO 88/10297, published Dec. 29, 1988, by Thomas et al; PCT PatentPublication No. WO 92/04445, published Mar. 19, 1992, by Thomas et al);and researchers have tried to express Group 1 proteins in recombinantexpression systems. Until the present invention, however, there has beenonly limited success in producing an active, easily purified recombinantmite Group 1 protein. For example, although researchers have tried toproduce active, fully functional recombinant Der f 1 and Der p 1proteins in E. coli, insect cells, and Saccharomyces cerevisiae, todate, none of these efforts has yielded an easily purified Group 1protein that binds to IgE in mite-allergic patients in a mannerequivalent to a native Group 1 protein.

Using E. coli, researchers expressed a recombinant Der p 1 protein as afusion protein with glutathione S transferase. The resulting recombinantprotein was produced in very low yields, at about 200 micrograms solubleprotein per liter of culture medium. Furthermore the GST-Der p 1 fusionprotein exhibited only about 50% of the IgE reactivity of the nativeprotein; see Chua et al, 1992, J Allergy Clin Immunol 89, 95-102.Moreover, this protein was expressed using a cDNA encoding the matureform, not the pro-form. The inventors are not aware of any reports ofsuccessful expression in E. coli of an active Der p 1 protein encoded bythe pro-form.

Using a baculovirus expression system in insect cells, Shoji et al,1996, Biosci Biotech Biochem 60, 621-625, and Shoji et al, 1997, BiosciBiotech Biochem 61, 1668-1673, reported production of a recombinant Derf 1 protein with IgE binding activity comparable to the native protein,but their process required an additional post-purification step ofeither acid or enzymatic treatment to cleave the pro-form to a matureform. This cleavage step was necessary because the Der f 1 pro-form hadonly 20% of the IgE reactivity of the native protein. To avoid the stepof acid proteolysis, Shoji et al. converted a glutamate at thecarboxyl-terminus of the “pro” region of the pro-form to a lysineresidue. This genetically engineered version of Der f 1 protein couldthen be cleaved with lysylendopeptidase to the mature form underconditions that did not result in the cleavage of internal lysines.However, this process is disadvantageous, especially at large scale, forproducing recombinant proteins. Controlling a relatively non-specificprotease cleavage step to cleave at only one specific site out ofseveral possible sites is inherently difficult. In addition, use of aprotease adds steps and cost to the purification process.

Using the yeast S. cerevisiae, Chua et al, ibid., produced recombinantDer p 1 protein. Although the Der p 1 protein was expressed as thepro-form in this system, the protein was not secreted by S. cerevisiae.As such, the resulting insoluble protein was purified using severalsteps, including solubilization, renaturation and affinitychromatography; such a process resulted in low yields of only about 1milligram protein per liter of yeast culture. Furthermore, the recoveredS. cerevisiae-expressed Der p 1 proenzyme exhibited only about 80% ofthe activity of native Der p 1 protein: Of 11 sera tested that werereactive with the native protein, only 9 were reactive with the S.cerevisiae expressed Der p 1 protein.

Thus, there remains a need in the art for an expression system thatproduces recombinant mite Group 1 proteins that exhibit activityequivalent to that of native mite Group 1 proteins. Preferably such asystem would allow for easy and cost-effective recovery of suchrecombinant proteins.

SUMMARY OF THE INVENTION

This invention relates to the surprising discovery that soluble, fullyactive mite Group 1 proteins can be expressed by a methyltrophic yeastmicroorganism. Also surprising is the finding that a methyltrophic yeastmicroorganism expresses a pro-form of a mite Group 1 protein that isefficiently processed and secreted, resulting in soluble, mature, fullyactive mite Group 1 protein in the culture medium.

This invention also relates to the unexpected discovery that a pro-formof a mite Group 1 protein allergen can be expressed in Escherichia coliand refolded such that the renatured protein has activity that is nearlyequivalent to a native Group 1 mite protein. Not only did this pro-formexhibit higher activity than previously reported for an E. coli-producedmature form of such a protein, but this is apparently the first reportof an active pro-form of a Group 1 mite protein.

The present invention provides a method to produce a recombinant miteGroup 1 protein, wherein the protein has a function of selectivelybinding IgE that binds to a native mite Group 1 protein and/or ofcausing proliferation of a T cell that proliferates in response to anative mite Group 1 protein, such a method including the steps of (a)culturing a methyltrophic yeast microorganism transformed with a nucleicacid molecule that encodes a mite Group 1 protein, and (b) recoveringthe expressed protein. Preferably such a protein is secreted into theculture the medium and has an IgE binding activity that is substantiallyequivalent to that of a native mite Group 1 protein. Preferredmethyltrophic yeast microorganisms include those of the genera Pichia,Hansenula, Torulopsis, and Candida, with those of the genus Pichia beingparticularly preferred. The present invention also includes a mite Group1 protein produced by such a method.

The present invention also provides a method to produce a recombinantmite Group 1 protein, wherein the protein has a function of selectivelybinding IgE that binds to a native mite Group 1 protein and/or ofcausing proliferation of a T cell that proliferates in response to anative mite Group 1 protein, such a method comprising the steps of (a)culturing an E. coli microorganism transformed with a nucleic acidmolecule encoding such a mite Group 1 protein, wherein the protein formsan inclusion body in the E. coli microorganism, (b) isolating such aninclusion body from such an E. coli microorganism, and (c) recoveringthe mite Group 1 protein from such an inclusion body, wherein therecovered mite Group 1 protein binds to IgE of at least about 70% ofserum samples comprising IgE that selectively bind to a native miteGroup 1 protein. Such a method preferably includes a refolding step. Thepresent invention also includes a mite Group 1 protein produced by sucha method.

Also included in the present invention is a method to detect miteallergy in an animal. Such a method includes the steps of (a) contactingan isolated mite Group 1 protein of the present invention with aputative IgE-containing substance under conditions suitable to form acomplex between the mite Group 1 protein and IgE and (b) determining thepresence of IgE reactive with the mite Group 1 protein by detecting thecomplex, wherein presence of reactive IgE is indicative of mite allergyin the animal. The present invention also includes a kit for detectionof mite allergy in an animal. Such a kit includes a mite Group 1 proteinof the present invention and a means for detecting IgE that selectivelybinds to a mite Group 1 protein.

One embodiment of the present invention is a composition that includes amite Group 1 protein of the present invention and an excipient. Alsoincluded is a method to use such a composition to reduce an allergicresponse to a mite Group 1 protein in a mite-allergic animal. Such amethod includes the step of administering such a composition to such ananimal.

Another embodiment of the present invention includes a methyltrophicyeast microorganism that includes a nucleic acid molecules encoding amite Group 1 protein operatively linked to a transcription controlsequence.

The present invention also includes isolated novel nucleic acidmolecules, recombinant molecules, and recombinant microorganisms thatcomprise at least one of the following nucleic acid sequences: SEQ IDNO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:34, SEQ IDNO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:42, SEQ IDNO:43, and SEQ ID NO:45. Also included in the present invention is anisolated protein having an amino acid sequence of SEQ ID NO:38 or SEQ IDNO:41, as well as nucleic acid molecules, recombinant molecules, andrecombinant microorganisms encoding such protein(s).

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a method to produce a recombinant miteGroup 1 protein that has at least one of the following functions (i.e.,activities, properties): (a) selectively binding IgE that binds to anative mite Group 1 protein; and (b) causing proliferation of a T cellthat proliferates in response to a native mite Group 1 protein. In oneembodiment, the method includes the steps of (a) culturing amethyltrophic yeast microorganism transformed with a nucleic acidmolecule that encodes a mite Group 1 protein, and (b) recovering therecombinant protein from the methyltrophic yeast microorganism. Inanother embodiment, the method includes the steps of (a) culturing an E.coli microorganism transformed with a nucleic acid molecule encoding amite Group 1 protein, wherein the protein forms an inclusion body in theE. coli microorganism, (b) isolating such an inclusion body from such anE. coli microorganism, and (c) recovering the mite Group 1 protein fromsuch an inclusion body, wherein the recovered mite Group 1 protein bindsto IgE of at least about 70% of serum samples comprising IgE thatselectively bind to a native mite Group 1 protein. The present inventionalso includes a recombinant mite Group 1 protein produced by either ofthese methods. Such a protein is referred to as a recombinant mite Group1 protein of the present invention, a mite Group 1 protein of thepresent invention, a Group 1 protein of the present invention, or aprotein of the present invention. Such a protein can be used in avariety of ways, such as those disclosed herein. For example, a proteinof the present invention can be used to detect mite allergy in ananimal, including detection of an animal suffering from mite allergy orof an animal susceptible to mite allergy. As another example, a proteinof the present invention can be used to reduce an allergic responseagainst a mite allergen (i.e., reduce mite allergy), includingprophylactic or therapeutic use. The present invention also includeskits and compositions that include at least one recombinant mite Group 1protein of the present invention. The present invention also includesmite Group 1 nucleic acid molecules, recombinant molecules, recombinantmicroorganisms and proteins, as disclosed herein.

As used herein, a mite refers to a minute arthropod of the orderAcarina, which includes a large assemblage of parasitic and free-livingorganisms. For example, astigmatic mites (Astigmata) are mostly involvedin commensal, symbiotic, or ectoparasitic relationships with otheranimals for at least part of their life cycle. There are at least twomajor lineages of astigmatic mites: Psoroptidia, which includes allspecies that are associated with skin, feathers, fur, and hair, such asectoparasitic feather mites and skin parasites of mammals; andPyroglyphidae, which includes mite species that are parasites of birdsand nest-dwelling commensals, as well as those species found in housedust. Allergen-producing astigmatic mites include Acarus siro,Aleuroglyphus ovatus, Blomia kulagini, Blomia tropicalis, Chortoglyphusarcuatus, Dermatophagoides farinae, Dermatophagoides microceras,Dermatophagoides pteronyssinus, Euroglyphus maynei, Glycyphagusdomesticus, Gohieria fusca, Lepidoglyphus destructor, Psoroptes ovis,Pterolichus obtusus, Sarcoptes scaiei, Tyrophagus longior, andTyrophagus putrescentiae. The main species of mite found in house dustare D. farinae and D. pteronyssinus, which together account for 80-90%of the total mite population generally found in houses. Additionally, B.kulagini, B. tropicalis, E. maynei, and T. longior are also found inhouses. As such, any mite is a suitable target for the products andmethods of the present invention. Preferred mites to target are of thegenera Blomia, Dermatophagoides, Euroglyphus, and Tyrophagus, with thoseof the species B. kulagini, B. tropicalis, D. farinae, D. pteronyssinus,E. maynei, and T. longior being more preferred. Particularly preferredmites to target are those mites of the genus Dermatophagoides, withthose of the species D. farinae and D. pteronyssinus being morepreferred.

One embodiment of the present invention is a method to produce arecombinant mite Group 1 protein, wherein the recombinant protein has afunction of selectively binding IgE that binds to native Group 1protein, and/or of causing proliferation of a T cell that proliferatesin response to a native mite Group 1 protein. It is to be noted that theterm “a” or “an” entity refers to one or more of that entity; forexample, a protein refers to one or more proteins or at least oneprotein; as another example, a nucleic acid molecule refers to one ormore nucleic acid molecules or at least one nucleic acid molecule. Assuch, the terms “a” or “an”, “one or more”, and “at least one” can beused interchangeably herein. It is also to be noted that the terms“comprising”, “including”, and “having” can be used interchangeablyherein. According to the present invention, an isolated, or biologicallypure, protein or nucleic acid molecule is a protein or nucleic acidmolecule, respectively, that has been removed from its natural milieu.As such, “isolated” and/or “biologically pure” do not necessarilyreflect the extent to which the protein or nucleic acid molecule hasbeen purified. An isolated protein or nucleic acid molecule of thepresent invention can be obtained from its natural source, can beproduced using recombinant nucleic acid technology, or can be producedby chemical synthesis.

A mite Group 1 protein refers to a Group 1 protein from (includingderived from) a species of mite. A recombinant mite Group 1 protein ofthe present invention refers to a mite Group 1 protein produced usingthe techniques of recombinant nucleic acid technology. A suitablerecombinant mite Group 1 protein of the present invention is a Group 1protein from any species of mite that is produced using recombinantnucleic acid techniques. Such species include, but are not limited to,Acarus siro, Aleuroglyphus ovatus, Blomia kulagini, Blomia tropicalis,Chortoglyphus arcuatus, Dermatophagoides farinae, Dermatophagoidesmicroceras, Dermatophagoides pteronyssinus, Euroglyphus maynei,Glycyphagus domesticus, Gohieria fusca, Lepidoglyphus destructor,Psoroptes ovis, Pterolichus obtusus, Sarcoptes scaiei, Tyrophaguslongior, and Tyrophagus putrescentiae. Preferred mite Group 1 proteinsof the present invention include those of the genera Blomia,Dermatophagoides, Euroglyphus, Lepidoglyphus, and Tyrophagus, with thoseof the species B. kulagini, B. tropicalis, D. farinae, D. microceras, D.pteronyssinus, E. maynei, L. destructor, and T. longior being morepreferred. Particularly preferred mite Group 1 proteins areDermatophagoides and Euroglyphus maynei Group 1 proteins, with D.farinae, D. pteronyssinus, and E. maynei Group 1 proteins being evenmore preferred.

In one embodiment, mite Group 1 proteins include, but are not limitedto, mite proteins that share homology with mite cysteine proteaseshaving molecular weights of about 25 HD, although such molecular weightsmay vary, for example due to genetic differences between species orpost-translation modifications.

As used herein, an isolated mite Group 1 protein may be a full-lengthprotein or any homolog of such a protein. An isolated mite Group 1protein of the present invention, including a homolog, can be identifiedin a straight-forward manner by the protein's ability to perform atleast one of the following functions: elicit an immune response against,or to, a mite Group 1 protein, bind to an IgE antibody (also referred toherein as IgE) reactive to a native mite Group 1 protein, bind to one ormore monoclonal antibodies that are reactive to a native mite Group 1protein, and/or stimulate proliferation of a T cell that proliferates inresponse to a native mite Group 1 protein. Examples of protein homologsof the present invention include mite Group 1 proteins of the presentinvention in which amino acids have been deleted (e.g. a truncatedversion of the protein, such as a peptide), inserted, inverted,substituted, and/or derivatized (e.g., by glycosylation,phosphorylation, acetylation, myristoylation, prenylation,palmitoylation, amidation, and/or addition of glycerophosphatidylinositol) such that the protein homolog exhibits one of theaforementioned functions. Homologs of mite Group 1 proteins of thepresent invention can be the result of natural allelic variation,including natural mutation. Protein homologs of the present inventioncan also be produced using techniques known in the art including, butnot limited to, direct modifications to the protein and/or modificationto a gene or nucleic acid molecule encoding the protein using, forexample, classic or recombinant DNA techniques to effect random ortargeted mutagenesis. Such nucleic acid molecules are referred to hereinas nucleic acid molecule homologs. A preferred recombinant mite Group 1protein of the present invention is a pro-form or a mature form of amite Group 1 protein.

A recombinant mite Group 1 protein of the present invention is a proteinthat is encoded by a mite Group 1 nucleic acid molecule of the presentinvention, also referred to as a nucleic acid molecule of the presentinvention. Such nucleic acid molecules are described in more detailherein. A recombinant mite protein of the present invention preferablyhas at least one of the following functions: (a) ability to selectivelybind IgE; and (b) ability to cause proliferation of a T cell thatproliferates in response to a native mite Group 1 protein. A native miteGroup 1 protein refers to a Group 1 protein recovered directly from aspecies of mite. In one embodiment, a native mite Group 1 protein ispurified from a mite extract under conditions that retain the mite Group1 protein's inherent IgE reactivity. As used herein, a protein's IgEreactivity refers to the ability of that protein to selectively bind IgEthat is reactive with a mite Group 1 protein. As used herein, the termsselectively binds IgE and selectively binds to (or with) IgE refer tothe ability of a mite Group 1 protein of the present invention topreferentially bind to IgE specific for Group 1 allergens, without beingable to substantially bind to IgE specific for other allergens. IgE thatis reactive with a mite Group 1 protein is an IgE antibody that reactswith a mite Group 1 protein in a manner equivalent to an IgE raised inresponse to a mite Group 1 protein. Methods to purify native mite Group1 proteins such that they retain their inherent (i.e., natural) IgEreactivity are known to those skilled in the art, examples of which aredisclosed herein. Such a native mite Group 1 protein can be used as a“standard” by which to compare a function, or activity, of a mite Group1 protein obtained by other means, such as by expression of arecombinant form of a mite Group 1 protein of the same species as thatfrom which the native protein is purified.

The ability of a recombinant mite Group 1 protein to selectively bind toIgE can be assayed by methods known in the art, such as, but not limitedto, those disclosed herein. Methods to compare that IgE binding activitywith the IgE binding activity of a native mite Group 1 protein are alsoknown in the art and include, but are not limited to, those methodsdisclosed herein. In one embodiment, recombinant and native forms of amite Group 1 protein are contacted (i.e., reacted) with serum samplesfrom animals that are allergic to mites using, for example, an ELISAformat, and a determination is made of what percentage of serum samplesreactive with the native protein are also reactive with the recombinantprotein. Preferably the testing is conducted using assay conditions inwhich essentially all of the mite-allergic serum samples give a positiveresult with the native mite Group 1 protein. An example of how thepercentage is determined is as follows: if a recombinant mite Group 1protein is tested against 10 mite-allergic serum samples, wherein all 10samples are reactive to a native mite Group 1 protein, and only 7samples are reactive to the recombinant protein, the reactivity isexpressed as 7/10, or 70%. That is, the recombinant mite Group 1 proteinselectively binds to IgE of 70% of serum samples comprising IgE thatselectively bind to a native mite Group 1 protein. As used herein, arecombinant mite Group 1 protein that has comparable, or substantiallyequivalent, activity to a native mite Group 1 protein is a recombinantmite Group 1 protein that reacts with essentially all of the serumsamples that are reactive with the native Group 1 protein.

In another embodiment, the abilities of recombinant and native forms ofa mite Group 1 protein to selectively bind to a monoclonal antibodyraised against a native mite Group 1 monoclonal antibody (i.e., ananti-native mite Group 1 monoclonal antibody) or to a panel of suchmonoclonal antibodies are compared. A recombinant Group 1 protein thathas comparable, or substantially equivalent, activity to a native Group1 protein is a recombinant mite Group 1 protein that reacts withessentially all of the monoclonal antibodies that react with the nativemite Group 1 protein. In the addition, the binding affinities of themonoclonal antibodies for the recombinant Group 1 protein should be verysimilar to the respective binding affinities of the monoclonalantibodies for the native Group 1 protein. The binding affinity can bedetermined with a simple dose-response curve.

A preferred method to determine the IgE reactivity of a recombinant miteGroup 1 protein is to compare the reactivities of recombinant and nativeforms of a mite Group 1 protein to IgE in serum samples that selectivelybind to native mite Group 1 proteins. The phrase, an IgE activitysubstantially equivalent to that of a native mite Group 1 protein refersto an IgE reactivity that is very comparable, or similar to, theactivity of a native mite Group 1 protein. Preferred mite Group 1proteins of the present invention exhibit IgE reactivities that are atleast about 70%, preferably at least about 75%, more preferably at leastabout 80%, more preferably at least about 85%, more preferably at leastabout 90%, and more preferably at least about 95% equivalent to a nativemite Group 1 protein. A particularly preferred recombinant mite Group 1protein of the present invention selectively binds to IgE of about 100%of serum samples comprising IgE that selectively bind to a native miteGroup 1 protein.

The ability of a recombinant mite Group 1 protein of the presentinvention to cause proliferation of a T cell that proliferates inresponse to a native mite Group 1 protein, also referred to herein as Tcell reactivity, can be assayed by methods known in the art; see, forexample, Janeway, et al., 1996, Immunobiology, Second Edition, GarlandPublishing Inc., New York, N.Y.; Janeway et al., ibid., is incorporatedby reference herein in its entirety. In one embodiment, a recombinantmite Group 1 protein of the present invention preferably contains mostor all of the relevant dominant T cell epitopes to stimulate T cellproliferation. In order to determine whether a recombinant mite Group 1protein contains relevant dominant T cell epitopes, T cell proliferationassays can be performed, by methods known to those skilled in the art,and the ability of that recombinant mite Group 1 protein to stimulate Tcell proliferation can be compared to the ability of the correspondingnative mite Group 1 protein to stimulate T cell proliferation. Apreferred recombinant mite Group 1 protein of the present inventionstimulates T cell proliferation as well as, or in a comparable mannerto, a native mite Group 1 protein.

A mite Group 1 nucleic acid molecule of the present invention refers toa Group 1 nucleic acid molecule derived from a mite, and as such, can beobtained from its natural source (i.e., directly from a mite, examplesof such mites being disclosed herein), or can be produced using, forexample, recombinant nucleic acid technology (e.g., polymerase chainreaction (PCR) amplification or cloning) or chemical synthesis. Anucleic acid molecule of the present invention can be DNA, RNA, or aderivative of DNA or RNA. Mite Group 1 nucleic acid molecules includenatural forms including allelic variants, complementary DNAs (cDNAs) orRNAs derived from genomic sequences (including those incorporatingnatural variations), and nucleic acid molecules modified by nucleotideinsertions, deletions, substitutions, and/or inversions in a manner suchthat the modifications do not substantially interfere with the nucleicacid molecule's ability to encode a mite Group 1 protein of the presentinvention. A modified mite Group 1 nucleic acid homolog can be producedusing a number of methods known to those skilled in the art, see, forexample, Sambrook et al, 1989, Molecular Cloning: A Laboratory Manual,Cold Spring Harbor Labs Press; Sambrook et al, ibid. is incorporated byreference herein in its entirety. For example, nucleic acid moleculescan be modified using a variety of techniques such as site-directedmutagenesis, chemical treatment, restriction enzyme cleavage, ligationof nucleic acid fragments, PCR amplification, synthesis ofoligonucleotide mixtures and ligation of mixture groups to “build” amixture of nucleic acid molecules, and combinations thereof. Nucleicacid molecules of the present invention can be selected by hybridizationwith a mite Group 1 nucleic acid molecule, as discussed below, and bythe ability of such nucleic acid molecules to encode a mite Group 1protein that selectively binds to IgE and/or causes proliferation of a Tcell that proliferates in response to a native mite roup 1 protein. Afull-length mite Group 1 protein, i.e., the initial translation product,is a pre-pro-form of the protein containing a pre-segment and apro-segment as well as the mature protein. The pre-segment, orpre-sequence, also known as the leader sequence or the signal sequence,apparently directs the mite Group 1 protein to be secreted from the celland is proteolytically cleaved to yield a pro-form of the protein. Thepro-segment, or pro-sequence, is then proteolytically cleaved to yieldthe mature Group 1 protein. A preferred protein to express is thepro-form (which includes the mature sequence as well as the prosequence, but does not have a signal sequence attached) or the matureform.

Nucleic acid molecules and proteins of the present invention that are ofcertain species and lengths are denoted as follows: a Der f 1 nucleicacid molecule protein of a certain length is denoted as nDerf1_(#), forexample, nDerf1₉₆₃, wherein “#” refers to the number of nucleotides inthat molecule; in a similar fashion, a Der p 1 nucleic acid molecule ofa certain length is denoted as nDerp1_(#), a E. maynei Group 1 nucleicacid molecule of a certain length is denoted as nEurm1_(#), and so on.Similarly, a Der f 1 protein of the present invention of known length isdenoted PDerf1_(#), a Der p 1 protein of the present invention of knownlength is denoted PDerp1_(#), a E. maynei Group 1 protein of a certainlength is denoted as PEurm1_(#), and so on.

A mite Group 1 nucleic acid molecule of the present invention includes anucleic acid molecule that hybridizes under stringent conditions with anucleic acid molecule having at least one of the following nucleic acidsequences: SEQ ID NO:3, SEQ ID NO:6, SEQ ID NO:9, SEQ ID NO:12, SEQ IDNO:15, SEQ ID NO:18, SEQ ID NO:21, SEQ ID NO:24, SEQ ID NO:27, SEQ IDNO:30, SEQ ID NO:33, SEQ ID NO:36, SEQ ID NO:39, SEQ ID NO:42, and SEQID NO:45.

SEQ ID NO:1 is the nucleic acid sequence of the coding strand ofnDerf1₉₆₃, a nucleic acid molecule that contains the coding sequence ofthe full-length, or pre-pro-form, of a Der f 1 protein. SEQ ID NO:4 isthe nucleic acid sequence of the coding strand of nDerf1_(909a), anucleic acid molecule that contains the coding sequence of the pro-formof a Der f 1 protein; the coding sequence of this pro-form protein spansfrom nucleotide 55 to nucleotide 963 of SEQ ID NO:1. SEQ ID NO:7 is thenucleic acid sequence of the coding strand of nDerf1_(669a), a nucleicacid molecule that contains the coding sequence of the mature form of aDer f 1 protein; the coding sequence of the mature form spans fromnucleotide 295 to nucleotide 963 of SEQ ID NO:1. Amino acid sequencesSEQ ID NO:2, SEQ ID NO:5, and SEQ ID NO:8 represent the amino acidsequences of Der f 1 proteins PDerf1₃₂₁, PDerf1_(303a), andPDerf1_(223a), respectively, which are the translation products ofnucleic acid sequences SEQ ID NO:1, SEQ ID NO:4, and SEQ ID NO:7respectively. Nucleic acid sequences SEQ ID NO:3, SEQ ID NO:6, and SEQID NO:9 represent reverse complements of SEQ ID NO:1, SEQ ID NO:4, andSEQ ID NO:7, respectively, and as such represent the non-coding strandsof nucleic acid molecules nDerf 1 nDerf1_(909a), and nDerf1_(669a),respectively.

SEQ ID NO:10 is the nucleic acid sequence of the coding strand ofnDerp1₉₆₀, a nucleic acid molecule that contains the coding sequence ofthe pre-pro-form of a Der p 1 protein. SEQ ID NO:13 is the nucleic acidsequence of the coding strand of nDerp1₉₀₆, a nucleic acid molecule thatcontains the coding sequence of the pro-form of a Der p 1 protein; thecoding sequence of this pro-form spans from nucleotide 55 to nucleotide960 of SEQ ID NO:10. SEQ ID NO:16 is the nucleic acid sequence of thecoding strand of nDerp1₆₆₉, a nucleic acid molecule that contains thecoding sequence of the mature form of a Der p1 protein; the codingsequence of this mature form spans from nucleotide 292 to nucleotide 960of SEQ ID NO:10. Amino acid sequences SEQ ID NO:11, SEQ ID NO:14, andSEQ ID NO:17 represent the amino acid sequences of Der p 1 proteinsPDerp1₃₂₀, PDerp1₃₀₂, and PDerp1₂₂₃, respectively, which are thetranslation products of nucleic acid sequences SEQ ID NO:10, SEQ IDNO:13, and SEQ ID NO:16, respectively. Nucleic acid sequences SEQ IDNO:12, SEQ ID NO:15, and SEQ ID NO:18 represent reverse complements ofSEQ ID NO:10, SEQ ID NO:13, and SEQ ID NO:16, respectively, and as such,represent the non-coding strands of nucleic acid molecules nDerp1₉₆₀,nDerp1₉₀₆, and nDerp1₆₆₉, respectively.

SEQ ID NO:19 is the nucleic acid sequence of the coding strand ofnEurm1₉₆₃, a nucleic acid molecule that contains the coding sequence ofthe pre-pro-form of a E. maynei Group 1 protein. SEQ ID NO:22 is thenucleic acid sequence of the coding strand of nEurm1₉₀₉, a nucleic acidmolecule that contains the coding sequence of the pro-form of a E.maynei Group 1 protein; the coding sequence of this pro-form spans fromnucleotide 55 to nucleotide 963 of SEQ ID NO:19. SEQ ID NO:25 is thenucleic acid sequence of the coding strand of nEurm1₆₆₉, a nucleic acidmolecule that contains the coding sequence of mature form of a E. mayneiGroup 1 protein; the coding sequence of this mature form spans fromnucleotide 295 to nucleotide 963 of SEQ ID NO:19. Sequences SEQ IDNO:20, SEQ ID NO:23 and SEQ ID NO:26 represent the amino acid sequencesof the E. maynei Group 1 proteins PEurm1₃₂₁, PEurm1₃₀₃, and PEurm1₂₂₃,respectively, which are the translation products of SEQ ID NO:19, SEQ IDNO:22, and SEQ ID NO:25, respectively. Nucleic acid sequences SEQ IDNO:21, SEQ ID NO:24, and SEQ ID NO:27 represent reverse complements ofSEQ ID NO:19, SEQ ID NO:22, and SEQ ID NO:25, respectively, and as such,represent the non-coding strands of nucleic acid molecules nEurm1₉₆₃,nEurm1₉₀₉, and nEurm1₆₆₉, respectively.

SEQ ID NO:28 is the nucleic acid sequence of the coding strand ofnDerf1_(909b) and represents a novel nucleic acid sequence. This nucleicacid sequence is derived from SEQ ID NO:4, but incorporates severalcodon changes to reflect codon preferences in Pichia. The changes are asfollows: a change from CGA to AGA in the codon spanning nucleotidepositions 538 to 540 of SEQ ID NO:4; a change from CGA to AGA in thecodon spanning nucleotide positions 547 to 549 of SEQ ID NO:4; a changefrom CGA to AGA in the codon spanning nucleotide positions 553 to 555 ofSEQ ID NO:4; and a change from CGA to AGA in the codon spanningnucleotide positions 556 to 558 of SEQ ID NO:4. SEQ ID NO:31 is thenucleic acid sequence of the coding strand of nDerf1_(669b) and alsorepresents a novel nucleic acid sequence. This nucleic acid sequence isderived from SEQ ID NO:7, but incorporates several codon changes, toreflect codon preferences in Pichia. The changes are as follows: changesfrom CGA to AGA in the codons spanning nucleotide positions (a) 298 to300, (b) 307 to 309, (c) 313 to 315, and (d) 316-318 of SEQ ID NO:7. SEQID NO:29 and SEQ ID NO:32 represent the amino acid sequences of proteinsPDerf1_(303b) and PDerf1_(223b), respectively, which are the translationproducts of nucleic acid sequences SEQ ID NO:28 and SEQ ID NO:31,respectively. SEQ ID NO:30 and SEQ ID NO:33 represent reversecomplements of SEQ ID NO:28 and SEQ ID NO:31, respectively.

SEQ ID NO:34 is the nucleic acid sequence of the coding strand ofnDerf1_(909c) and represents a novel nucleic acid sequence. This nucleicacid sequence is derived from SEQ ID NO:4, but incorporates severalcodon changes to reflect codon preferences in E. coli. The first changeis from CCA to CCG in the codon spanning nucleotide positions 4 to 6 ofSEQ ID NO:4; the second change is from CGA to CGT in the codon spanningnucleotide positions 547 to 549 of SEQ ID NO:4; the third is from CGA toCGT in the codon spanning nucleotide positions 553 to 555 of SEQ IDNO:4; the fourth is from CGA to CGT in the codon spanning nucleotidepositions 556 to 558 of SEQ ID NO:4; and the fifth is from TAT to TAC inthe codon spanning nucleotide positions 895 to 897 of SEQ ID NO:4 toeliminate a NdeI cloning site within the Der f 1 coding region. SEQ IDNO:43 is the nucleic acid sequence of the coding region of nDerf1_(669d)and also represents a novel nucleic acid sequence. This nucleic acidsequence is derived from SEQ ID NO:7, but incorporates several codonchanges to reflect codon preferences in E. coli. The first change is achange from CGA to CGT in the codon spanning nucleotide positions 307 to309 of SEQ ID NO:7; the second is from CGA to CGT in the codon spanningnucleotide positions 313 to 315 of SEQ ID NO:7; the third is from CGA toCGT in the codon spanning nucleotide positions 316 to 318 of SEQ IDNO:7; and the fourth is from TAT to TAC in the codon spanning nucleotidepositions 655 to 657 of SEQ ID NO:7 to eliminate a NdeI cloning sitewithin the Der f 1 coding region. Sequences SEQ ID NO:35 and SEQ IDNO:44 represent the amino acid sequences of proteins PDerf1_(303c) andPDerf1_(223d), respectively, and are the translation products of nucleicacid sequences SEQ ID NO:34 and 43, respectively. SEQ ID NO:36 and SEQID NO:45 represent reverse complements of SEQ ID NO:34 and SEQ ID NO:43,respectively.

SEQ ID NO:37 is the nucleic acid sequence of the coding strand ofnDerf1_(909d) and represents a novel nucleic acid sequence. This nucleicacid sequence is derived from SEQ ID NO:28, the D. farinae pro-formGroup 1 protein with codons altered to reflect Pichia codon preferencesdescribed above; however, SEQ ID NO:37 has also been altered to changethe codon spanning nucleotide positions 397 to 399 of SEQ ID NO:28 fromAAC (encoding asparagine (N)) to CAA (encoding glutamine (Q)). Thischange results in the encoding of a protein that lacks an N-linkedglycosylation site. Thus, translation of SEQ ID NO:37 yields amino acidsequence SEQ ID NO:38 which is representative of protein PDerf1_(303d),which is a novel protein, with the N to Q change at position 133 of theamino acid sequence. SEQ ID NO:39 represents the reverse complement ofSEQ ID NO:37.

SEQ ID NO:40 is the nucleic acid sequence of the coding strand ofnDerf1₆₆₉, and represents a novel nucleic acid sequence. This nucleicacid sequence is derived from SEQ ID NO:31, the D. farinae mature formGroup 1 protein with codons altered to reflect Pichia codon preferencesdescribed above; however, SEQ ID NO:40 has also been altered to changethe codon spanning nucleotide positions 157 to 159 of SEQ ID NO:31 fromAAC (encoding asparagine (N)) to CAA (encoding glutamine (Q)). Thischange results in the encoding of a protein that lacks an N-linkedglycosylation site. Thus, translation of SEQ ID NO:40 yields amino acidsequence SEQ ID NO:41 which is representative of protein PDerf1_(223c),which is a novel protein, with the N to Q change at position 53 of theamino acid sequence. SEQ ID NO:42 represents the reverse complement ofSEQ ID NO:40.

As stated above, a mite Group 1 nucleic acid molecule of the presentinvention includes a nucleic acid molecule that hybridizes understringent conditions with a nucleic acid molecule having a specifiednucleic acid sequence. Stringent hybridization conditions are determinedbased on defined physical properties of the gene or other nucleic acidmolecule to which the nucleic acid molecule to be tested is beinghybridized, and can be defined mathematically. Stringent hybridizationconditions are those experimental parameters that allow an individualskilled in the art to identify significant similarities betweenheterologous nucleic acid molecules. These conditions are well known tothose skilled in the art. See, for example, Sambrook, et al., 1989,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press,and Meinkoth, et al., 1984, Anal. Biochem. 138, 267-284, each of whichis incorporated by reference herein in its entirety. As explained indetail in the cited references, the determination of hybridizationconditions involves the manipulation of a set of variables including theionic strength (M, in moles/liter), the hybridization temperature (°C.), the concentration of nucleic acid helix destabilizing agents (suchas formamide), the average length of the shortest hybrid duplex (n), andthe percent G+C content of the fragment to which an unknown nucleic acidmolecule is being hybridized. For nucleic acid molecules of at leastabout 150 nucleotides, these variables are inserted into a standardmathematical formula to calculate the melting temperature, or T₁, of agiven nucleic acid molecule. As defined in the formula below, T_(m) isthe temperature at which two complementary nucleic acid molecule strandswill disassociate, assuming 100% complementarity between the twostrands:

T _(m)=81.5° C.+16.6 log M+0.41(%G+C)−500/n−0.61(% formamide).

For nucleic acid molecules smaller than about 50 nucleotides, hybridstability is defined by the dissociation temperature (T_(d)), which isdefined as the temperature at which 50% of the duplexes dissociate. Forthese smaller molecules, the stability at a standard ionic strength isdefined by the following equation:

T _(d)=4(G+C)+2(A+T).

A temperature of 5° C. below T_(d) is used to detect hybridizationbetween perfectly matched molecules.

Also well known to those skilled in the art is how base pair mismatch,i.e. differences between two nucleic acid molecules being compared,including non-complementarity of bases at a given location, and gaps dueto insertion or deletion of one or more bases at a given location oneither of the nucleic acid molecules being compared, will affect T_(m)or T_(d) for nucleic acid molecules of different sizes. For example,T_(m) decreases about 1° C. for each 1% of mismatched base pairs forhybrids greater than about 150 bp, and T_(d) decreases about 5° C. foreach mismatched base pair for hybrids below about 50 bp. Conditions forhybrids between about 50 and about 150 base pairs can be determinedempirically and without undue experimentation using standard laboratoryprocedures well known to those skilled in the art. These simpleprocedures allow one skilled in the art to set the hybridizationconditions (by altering, for example, the salt concentration, theformamide concentration or the temperature) so that only nucleic acidhybrids with greater than a specified % base pair mismatch willhybridize. Stringent hybridization conditions are commonly understood bythose skilled in the art to be those experimental conditions that willallow less than or equal to about 30% base pair mismatch (i.e., at leastabout 70% identity). Because one skilled in the art can easily determinewhether a given nucleic acid molecule to be tested is less than orgreater than about 50 nucleotides, and can therefore choose theappropriate formula for determining hybridization conditions, he or shecan determine whether the nucleic acid molecule will hybridize with agiven gene under stringent hybridization conditions and similarlywhether the nucleic acid molecule will hybridize under conditionsdesigned to allow a desired amount of base pair mismatch.

Hybridization reactions are often carried out by attaching the nucleicacid molecule to be hybridized to a solid support such as a membrane,and then hybridizing with a labeled nucleic acid molecule, typicallyreferred to as a probe, suspended in a hybridization solution. Examplesof common hybridization reaction techniques include, but are not limitedto, the well-known Southern and northern blotting procedures. Typically,the actual hybridization reaction is done under non-stringentconditions, i.e., at a lower temperature and/or a higher saltconcentration, and then high stringency is achieved by washing themembrane in a solution with a higher temperature and/or lower saltconcentration in order to achieve the desired stringency.

For example, if the skilled artisan wished to identify a nucleic acidmolecule that hybridizes under conditions that would allow less than orequal to 30% pair mismatch with a nucleic acid molecule of about 150 bpin length or greater, the following conditions could preferably be used.The unknown nucleic acid molecules would be attached to a supportmembrane, and the 150 bp probe would be labeled, e.g. with a radioactivetag. The hybridization reaction could be carried out in a solutioncomprising 2×SSC and 0% formamide, at a temperature of about 37° C. (lowstringency conditions). Solutions of differing concentrations of SSC canbe made by one of skill in the art by diluting a stock solution of20×SSC (175.3 gram NaCl and about 88.2 gram sodium citrate in 1 liter ofwater, pH 7) to obtain the desired concentration of SSC. The skilledartisan would calculate the washing conditions required to allow up to30% base pair mismatch. For example, assuming an average G+C content ofthe nucleic acid molecule to be hybridized of about 50%, and a washsolution comprising 1×SSC and 0% formamide, the T_(m) of perfect hybridswould be about 85° C.:

81.5° C.+16.6 log(0.15M)+(0.41×0.37)−(500/150)−(0.61×0)=85° C.

Thus, to achieve hybridization with nucleic acid molecules having about30% base pair mismatch, hybridization washes would be carried out at atemperature of less than or equal to 55° C. It is thus within the skillof one in the art to calculate additional hybridization temperaturesbased on the desired percentage base pair mismatch, formulae and G/Ccontent disclosed herein. For example, it is appreciated by one skilledin the art that as the nucleic acid molecule to be tested forhybridization against nucleic acid molecules of the present inventionhaving sequences specified herein becomes longer than 150 nucleotides,the T_(m) for a hybridization reaction allowing up to 30% base pairmismatch will not vary significantly from 55° C. It is to be noted thatthe minimal size of a mite Group 1 nucleic acid molecule of the presentinvention is a size sufficient to allow the formation of a stable hybrid(i.e., hybridization under stringent hybridization conditions) with thecomplementary sequence of another nucleic acid molecule. As such, theminimal size of a mite Group 1 nucleic acid molecule of the presentinvention is from about 12 to about 18 nucleotides in length.

Furthermore, it is known in the art that there are commerciallyavailable computer programs for determining the degree of similaritybetween two nucleic acid or protein sequences. These computer programsinclude various known methods to determine the percentage identity andthe number and length of gaps between hybrid nucleic acid molecules orproteins. Preferred methods to determine the percent identity amongamino acid sequences and also among nucleic acid sequences includeanalysis using one or more of the commercially available computerprograms designed to compare and analyze nucleic acid or amino acidsequences. These computer programs include, but are not limited to, theWisconsin Package Version 9.0 sequence analysis software, available fromGenetics Computer Group (GCG™), Madison, Wis.; DNAsis™, available fromHitachi Software, San Bruno, Calif.; and MacVector™, available from theEastman Kodak Company, New Haven, Conn. A preferred method to determinepercent identity among amino acid sequences and also among nucleic acidsequences includes using the GAP program with pair-wise comparisonswithin the GCG™ Wisconsin Package Version 9.0 sequence analysissoftware, hereinafter referred to as default parameters.

Preferred mite Group 1 proteins of the present invention includerecombinant mite Group 1 proteins that are at least about 70%,preferably at least about 75%, more preferably at least about 80%, morepreferably at least about 85%, more preferably at least about 90%, andeven more preferably at least about 95% identical to amino acidsequences SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ IDNO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ IDNO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, and SEQID NO:44, and/or a protein comprising a fragment of any of these aminoacid sequences, wherein the fragment has a function of selectivelybinding to IgE that binds native mite Group 1 protein and/or causingproliferation of a T cell that proliferates in response to a native miteGroup 1 protein. A particularly preferred mite Group 1 protein includesat least a portion of at least one of the following amino acidsequences: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ IDNO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ IDNO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, and/orSEQ ID NO:44. Also preferred is a protein comprising at least a portionof at least one protein encoded by an allelic variant of a nucleic acidmolecule encoding a protein having at least one of the followingsequences: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:11, SEQ IDNO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ IDNO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ ID NO:38, SEQ ID NO:41, and/orSEQ ID NO:44. Such portions preferably have at least one of thefollowing functions: selectively binding to IgE that binds native miteGroup 1 protein and/or causing proliferation of a T cell thatproliferates in response to a native mite Group 1 protein. It is to benoted that the proteins corresponding to SEQ ID NO:2, SEQ ID NO:5, SEQID NO:8, SEQ ID NO:11, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQ IDNO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ IDNO:38, SEQ ID NO:41, and/or SEQ ID NO:44 are, respectively, PDerf1₃₂₁,PDerf1_(303a), PDerf1_(223a), PDerp1₃₂₀, PDerp1₃₀₂, PDerp1₂₂₃,PEurm1₃₂₁, PEurm1₃₀₃, PEurm1₂₂₃, PDerf11_(303b), PDerf1_(223b),PDerf1_(303c), PDerf1_(303d), PDerf1_(223c), and/or PDerf_(223d).

Preferred nucleic acid molecules to use in encoding mite Group 1proteins of the present invention are nucleic acid molecules that are atleast about 70%, preferably at least about 75%, more preferably at leastabout 80%, more preferably at least about 85%, more preferably at leastabout 90%, more preferably at least about 95%, and even more preferablyabout 100% identical to nucleic acid sequences SEQ ID NO:1, SEQ ID NO:4,SEQ ID NO:7, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:16, SEQ ID NO:19, SEQID NO:22, SEQ ID NO:25, SEQ ID NO:28, SEQ ID NO:31, SEQ ID NO:34, SEQ IDNO:37, SEQ ID NO:40, and SEQ ID NO:43, and/or a fragment thereof,wherein such a fragment (a) hybridizes to a nucleic acid molecule havingthe complement of any of the listed nucleic acid sequences and/or (b)encodes a protein that selectively binds to IgE that binds native miteGroup 1 protein and/or causes proliferation of a T cell thatproliferates in response to a native mite Group 1 protein. Particularlypreferred mite Group 1 nucleic acid molecules include at least one ofthe following nucleic acid sequences: SEQ ID NO:1, SEQ ID NO:4, SEQ IDNO:7, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:16, SEQ ID NO:19, SEQ IDNO:22, SEQ ID NO:25, SEQ ID NO:28, SEQ ID NO:31, SEQ ID NO:34, SEQ IDNO:37, SEQ ID NO:40, and SEQ ID NO:43, and fragments thereof. Alsopreferred are naturally occurring variants of such nucleic acidmolecules, and fragments thereof. It is to be noted that SEQ ID NO:1,SEQ ID NO:4, SEQ ID NO:7, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:16, SEQID NO:19, SEQ ID NO:22, SEQ ID NO:25, SEQ ID NO:28, SEQ ID NO:31, SEQ IDNO:34, SEQ ID NO:37, SEQ ID NO:40, and SEQ ID NO:43 are the codingstrands of the following respective nucleic acid molecules: nDerf1₉₆₃,nDerf1_(909a), nDerf1_(669a), nDerp1₉₆₀, nDerp1₉₀₆, nDerp1₆₆₉,nEurm1₉₆₃, nEurm1₉₀₉, nEurm1₆₆₉, nDerf11_(909b), nDerf1_(669b),nDerf1_(909c), nDerf1_(909d), nDerf1_(669c), and/or nDerf_(669d).

One embodiment of a method to produce a recombinant mite Group 1 proteinof the present invention includes the steps of (a) culturing amethyltrophic yeast microorganism transformed with a nucleic acidmolecule encoding the recombinant mite Group 1 protein, and (b)recovering the recombinant mite Group 1 protein from the methyltrophicyeast microorganism. A methyltrophic yeast microorganism is a yeaststrain capable of using methanol as its sole carbon source. Although anymethyltrophic yeast can be used in the methods of the present invention,preferred methyltrophic yeast microorganisms to transform and cultureinclude those of the genera Pichia, Hansenula, Torulopsis, and Candida,with the genus Pichia being particularly preferred. Preferredmethyltrophic yeast species include Pichia pastoris, Pichia acaciae,Pichia anomala, Pichia augusta, Pichia capsulata, Pichia fabianii,Pichia farinosa, Pichia guilliermondii, Pichia methanolica, Pichianorvegensis, Pichia pinus, Pichia stipitis, Hansenula polymorpha, andCandida boidinii. A preferred Pichia microorganism is Pichia pastorisAnother embodiment of a method to produce a recombinant mite Group 1protein of the present invention includes the steps of (a) culturing anE. coli microorganism transformed with a nucleic acid molecule encodingthe recombinant mite Group 1 protein under conditions in which theprotein forms an inclusion body in the E. coli microorganism, (b)isolating the inclusion body from the E. coli microorganism, and (c)recovering the recombinant mite Group 1 protein from the inclusion body.Such a recombinant mite Group 1 protein selectively binds to IgE of atleast about 70% of IgE-containing serum samples that selectively bind toa native mite Group 1 protein.

Transformation of a nucleic acid molecule of the present invention intoa microorganism can be accomplished by any method by which a nucleicacid molecule can be inserted into the cell. Transformation techniquesinclude, but are not limited to, transfection, electroporation,microinjection, lipofection, adsorption, and protoplast fusion.Transformed nucleic acid molecules of the present invention can remainextrachromosomal or can integrate into one or more sites within achromosome of the transformed (i.e., recombinant) microorganism in sucha manner that their ability to be expressed is retained. A transformedmicroorganism is also referred to herein as a transformed cell, arecombinant microorganism or a recombinant cell.

A microorganism to be transformed can be either an untransformed cell ora cell that is already transformed with at least one nucleic acidmolecule (e.g., one or more nucleic acid molecules encoding one or moreproteins of the present invention and/or other proteins). A recombinantmicroorganism of the present invention is preferably produced bytransforming a host cell with one or more recombinant moleculescomprising one or more nucleic acid molecules of the present invention.Examples of recombinant microorganisms are provided herein.

As used herein, a recombinant molecule comprises a nucleic acid moleculeof the present invention operatively linked to a transcription controlsequence, preferably contained within an expression vector. The phraseoperatively linked refers to joining of a nucleic acid molecule to atranscription control sequence in a manner such that the molecule isable to be expressed when transformed into a yeast or E. colimicroorganism. As used herein, an expression vector is a DNA or RNAvector, typically either a plasmid or viral genome, that is capable oftransforming a cell and of effecting expression of a specified nucleicacid molecule. A preferred recombinant molecule of the present inventioncontains regulatory sequences such as transcription control sequences,translation control sequences, origins of replication, and otherregulatory sequences that are compatible with the recombinantmicroorganism and that control the expression of nucleic acid moleculesof the present invention. In particular, recombinant molecules of thepresent invention at least include transcription control sequences.Transcription control sequences are sequences which control theinitiation, elongation, and termination of transcription. Particularlyimportant transcription control sequences are those which controltranscription initiation, such as promoter, enhancer, operator andrepressor sequences. Suitable transcription control sequences includeany transcription control sequence that can function in at least one ofthe recombinant microorganisms of the present invention. A variety ofsuch transcription control sequences are known to those skilled in theart; examples included, but are not limited to, tac, lac, trp, trc,oxy-pro, omp/lpp, rrnB, bacteriophage lambda (such as lambda p_(L) (alsoreferred to herein as lambda PL) and lambda p_(R) (also referred toherein as lambda PR) and fusions that include such promoters),bacteriophage T7, T7lac, bacteriophage T3, bacteriophage SP6, SP01,alpha-mating factor, Pichia alcohol oxidase (AOX), antibiotic resistancegene, as other sequences capable of controlling gene expression in E.coli or methyltrophic yeast microorganisms; it is to be noted that thislist is not intended to be limiting as many additional transcriptionalcontrol sequences are known. A particularly preferred recombinantmolecule includes a nucleic acid molecule that encodes a mite Group 1protein, operatively linked to the alcohol oxidase promoter AOX1.Another particularly preferred recombinant molecule includes a nucleicacid molecule that encodes a mite Group 1 protein operatively linked tothe lambda PL promoter or the lambda PR promoter.

Recombinant molecules of the present invention can contain secretorysignals (i.e., signal segment nucleic acid sequences) to enable anexpressed fusion protein of the present invention to be secreted fromthe cell that produces the protein. Examples of suitable signal segmentsinclude any signal segment capable of directing the secretion of aprotein of the present invention. Preferred signal segment sequencesinclude, but are not limited to, mite Group 1 protein natural signalsequences and yeast alpha signal sequences, with the S. cerevisiae alphasignal sequence being particularly preferred for expression of apro-form of a mite Group 1 protein in a methyltrophic yeastmicroorganism.

Another embodiment of the present invention includes a recombinantvector, which includes at least one isolated nucleic acid molecule ofthe present invention, inserted into any vector capable of deliveringthe nucleic acid molecule into a host cell. Such a vector containsheterologous nucleic acid sequences, that is nucleic acid sequences thatare not naturally found adjacent to nucleic acid molecules of thepresent invention and that preferably are derived from a species otherthan the species from which the nucleic acid molecule(s) are derived.The vector can be either RNA or DNA, either prokaryotic or eukaryotic,and typically is a virus or a plasmid. Recombinant vectors can be usedin the cloning, sequencing, and/or otherwise manipulation of mite Group1 nucleic acid molecules of the present invention.

Recombinant DNA technologies can be used to improve expression oftransformed nucleic acid molecules by manipulating, for example, thenumber of copies of the nucleic acid molecules within a host cell, theefficiency with which those nucleic acid molecules are transcribed, theefficiency with which the resultant transcripts are translated, and theefficiency of post-translational modifications. Recombinant techniquesuseful for increasing the expression of nucleic acid molecules of thepresent invention include, but are not limited to, operatively linkingnucleic acid molecules to high-copy number plasmids, integration of thenucleic acid molecules into one or more host cell chromosomes, additionof vector stability sequences to plasmids, substitutions ormodifications of transcription control signals (e.g., promoters,operators, enhancers), substitutions or modifications of translationalcontrol signals (e.g., ribosome binding sites, Shine-Dalgarnosequences), modification of nucleic acid molecules of the presentinvention to correspond to the codon usage of the host cell, deletion ofsequences that destabilize transcripts, and use of control signals thattemporally separate recombinant cell growth from recombinant enzymeproduction during fermentation. The activity of an expressed recombinantprotein of the present invention may be improved by fragmenting,modifying, or derivatizing nucleic acid molecules encoding such aprotein.

One embodiment of a mite Group 1 protein of the present invention is afusion protein. Suitable fusion segments for use with the presentinvention include, but are not limited to, segments that can: link twoor more mite Group 1 proteins of the present invention to formmultimers; enhance a protein's stability; facilitate the purification ofa mite Group 1 protein; and/or to affect the immune response to a miteGroup 1 protein. A suitable fusion segment can be a domain of any sizethat has the desired function (e.g., imparts increased stability,imparts increased immunogenicity to a protein, and/or simplifiespurification of a protein). Fusion segments can be joined to aminoand/or carboxyl termini of the mite Group 1 protein and can besusceptible to cleavage in order to enable straight-forward recovery ofa mite Group 1 protein. Fusion proteins are preferably produced byculturing a recombinant cell transformed with a fusion nucleic acidmolecule that encodes a protein including the fusion segment attached toeither the carboxyl and/or amino terminal end of a mite Group 1 protein.Preferred fusion segments include a metal binding domain (e.g., apoly-histidine segment); an immunoglobulin binding domain (e.g., ProteinA; Protein G; T cell; B cell; Fc receptor or complement proteinantibody-binding domains); a sugar binding domain (e.g., a maltosebinding domain); and/or a “tag” domain (e.g., at least a portion of-galactosidase, a strep tag peptide, a T7 tag peptide, a Flag™ peptide,or other domains that can be purified using compounds that bind to thedomain, such as monoclonal antibodies). More preferred fusion segmentsinclude metal binding domains, such as a poly-histidine segment; amaltose binding domain; a strep tag peptide, such as that available fromBiometra in Tampa, Fla.; and an S10 peptide.

An important discovery of the present invention are methods identifiedto produce recombinant mite Group 1 proteins having desirable functions.For example, culturing of a methyltrophic yeast microorganismtransformed with a nucleic acid molecule encoding a pro-form of a miteGroup 1 protein fused to an alpha factor signal sequence results in theproduction of a mature mite Group 1 protein exhibiting IgE reactivitycomparable to that exhibited by the corresponding native mite Group 1protein. Such culturing leads not only to expression of the pro-form ofthe protein but also to processing of the pro-form into the mature form.This result was unexpected in that P. pastoris expression of a cDNAencoding pro-cathepsin B, in contrast, yielded the pro-form of theenzyme which needed to be activated in vitro in the presence of acid;see, for example, Illy et al, 1997, J Biol Chem 272, 1197-1202, andreferences cited therein. In another example, culturing of an E. colimicroorganism transformed with a nucleic acid molecule encoding apro-form of a mite Group 1 protein results in the production ofinclusion bodies comprising the pro-form, which is then recovered bysolubilizing and refolding the protein. The recovered pro-form exhibitsIgE reactivity that is at least 70% equivalent to that exhibited by thecorresponding native mite Group 1 protein.

Effective culturing conditions to produce a recombinant mite Group 1protein of the present invention include, but are not limited to,effective media, bioreactor, temperature, pH and oxygen conditions thatpermit protein production. An effective medium refers to any medium inwhich a cell is cultured to produce a mite Group 1 protein of thepresent invention. Such a medium typically comprises an aqueous mediumhaving assimilable carbon, nitrogen and phosphate sources, andappropriate salts, minerals, metals and other nutrients, such asvitamins. Cells of the present invention can be cultured in conventionalfermentation bioreactors, shake flasks, test tubes, microtiter dishes,and petri plates. Culturing can be carried out at a temperature, pH andoxygen content appropriate for methyltrophic yeast or E. coli. Suchculturing conditions are within the expertise of one of ordinary skillin the art, and examples are provided in the Examples section.

Depending on the vector and host system used for production, resultantproteins of the present invention may either remain within therecombinant cell; be secreted into the culturing, or fermentation,medium; or be secreted into a space between two cellular membranes. Inaccordance with the present invention, recombinant mite Group 1 proteinsproduced by a methyltrophic yeast microorganism of the present inventionare preferably secreted into the culturing medium, and recombinant miteGroup 1 proteins produced by E. coli form inclusion bodies within the E.coli microorganism. As used herein, recovering a protein from amethyltrophic yeast microorganism refers to collecting the mediumcontaining the yeast and the protein and need not imply additional stepsof separation or purification. In a preferred embodiment, the protein isin the medium and, hence, can be easily separated from the yeast. Also,as used herein, the phrases isolating an inclusion body from an E. colimicroorganism or recovering protein from the inclusion bodies do notimply any specified degree of separation or purification.

Proteins of the present invention can be purified using a variety ofpurification techniques, such as, but not limited to, affinitychromatography, ion exchange chromatography, filtration,electrophoresis, hydrophobic interaction chromatography, gel filtrationchromatography, reverse phase chromatography, concanavalin Achromatography, chromatofocusing and differential solubilization.Proteins of the present invention are preferably retrieved in“substantially pure” form. As used herein, “substantially pure” refersto a purity that allows for the effective use of the protein as adiagnostic, therapeutic or prophylactic.

A preferred method to purify a mite Group 1 protein from a mite Group 1transformed-methyltrophic yeast microorganism is to recover the mediumin which the mite Group 1 transformed methyltrophic yeast microorganismwas cultured, and then to purify the mite Group 1 protein usingconventional chromatography techniques. Preferred is a method by whichthe culturing medium is subjected to ion-exchange chromatography.Preferred ion-exchange resins to use include cationic ion-exchangeresins, particularly SP-Sepharose (available from Amersham-PharmaciaBiotech, Piscataway, N.J.) at about pH 4.5.

A preferred method to produce a recombinant mite Group 1 protein in E.coli is to culture a transformed E. coli microorganism of the presentinvention under conditions that cause the mite Group 1 protein to forman inclusion body within the microorganism. Such conditions are known inthe art, and examples of such conditions are described in the Examplessection, below. An inclusion body, as used herein, is a highlyaggregated, insoluble form of a mite Group 1 protein present in the E.coli microorganism. These inclusion bodies are thought to containmis-folded (i.e., improperly folded) denatured protein. Mite Group 1protein inclusion bodies are then recovered by lysing the E. colimicroorganisms. Methods to recover inclusion bodies and purify andrefold E. coli expressed proteins are known in the art, see, forexample, Deutscher, ed., 1990, Guide to Protein Purification AcademicPress, San Diego, Calif., which is incorporated by reference herein inits entirety. Methods to lyse E. coli are known in the art, and includemethods such as enzymatic lysis, mechanical lysis, and liquid shearlysis; see, for example, Deutscher, ibid. A preferred method to lysetransformed E. coli is by mechanical means, most preferably with amicrofluidizer. Insoluble proteins can be recovered by centrifugation.To solubilize the insoluble proteins, a variety of reagents can be used.Suitable reagents include: guanidine-hydrochloride (HCl), preferably ata pH from about pH 7 to about pH 8 and at a concentration of from about5 molar (M) to about 8 M; urea, preferably at a concentration of fromabout 6 M to about 8 M; sodium dodecyl sulfate; alkaline pH (greaterthan pH 9); and/or acetonitrile/propanol. Preferred methods tosolubilize include use of 8 M urea in Tris buffer, pH 9.5, in 100millimolar (mM) β-mercaptoethanol. Solubilized proteins can be refoldeddirectly or subjected to additional purification step(s). A preferredmethod is to purify the mite Group 1 protein further before refolding.Any number of different types of resins suitable for proteinpurification may be used; preferred is an anion-exchange type resin suchas, for example, Q-SEPHAROSE™ resin (available from Amersham-PharmaciaBiotech). To refold the solubilized protein directly or afterpurification, a number of methods are known in the art; see, forexample, Deutscher, M. (1990), ibid. The term, refold, as used herein,refers to conditions in which reduced proteins can revert to theircorrect conformations, including restoring the correct disulfidebridges. Preferred methods to refold include (a) using glutathione toform mixed disulfides and/or (b) using high pH. For method (a), stepsinvolved include: (i) reduction of the protein with a reducing agent,such as dithiothreitol, preferably 6 mM dithiothreitol for at leastabout 30 minutes; (ii) addition of oxidized glutathione, preferably at aconcentration of from about 25 mM to about 100 mM, with about 25 mMbeing particularly preferred; (iii) dilution of the mixture to a ureaconcentration of preferably between about 0.5 M and 1 M, with 0.75 Murea being particularly preferred (assuming solubilization is conductedin the presence of urea) using a buffer, preferably 50 mM Tris, pH 9.5,with the addition of from about 5 mM to about 25 mM, preferably 6.5 mM,cysteine or reduced glutathione; (iv) incubation for about 10 to about20 hours at 4° C.; and (v) dialysis against a buffer to remove urea;preferred buffers are phosphate buffered saline (PBS) at about pH 7.5 or50 mM Tris-HCl, pH 7.5. For method (b), steps involved include: (i)adjusting pH of the solubilized protein to about pH 10; (ii) reducingthe protein by treatment with 100 mM β-mercaptoethanol; and (iii)refolding by dialysis against PBS, pH 7.2 or 50 mM Tris-HCl, pH 7.5.

One embodiment of the present invention is a methyltrophic yeastmicroorganism comprising a mite Group 1 nucleic acid molecule of thepresent invention operatively linked to a transcription controlsequence. Examples of suitable yeast strains, nucleic acid molecules andtranscription control sequences are described herein. A preferred yeastis of the genus Pichia, with the species Pichia pastoris being even morepreferred.

Another embodiment of the present invention is an isolated nucleic acidmolecule comprising a nucleic acid sequence selected from the groupconsisting of SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33,SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40,SEQ ID NO:42, SEQ ID NO:43, and/or SEQ ID NO:45. Also included arerecombinant molecules that comprise a nucleic acid molecule selectedfrom the group consisting of SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31,SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39,SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:43, and/or SEQ ID NO:45,operatively linked to a transcription control sequence. Examples ofsuitable transcription control sequences are described herein. Alsoincluded in the present invention is a recombinant microorganismcomprising a nucleic acid molecule selected from the group consisting ofSEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:34,SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:42,SEQ ID NO:43, and SEQ ID NO:45. Suitable host cells to transform includeany cell that can be transformed with a nucleic acid molecule of thepresent invention. Host cells can be either untransformed cells or cellsthat are already transformed with at least one nucleic acid molecule(e.g., nucleic acid molecules encoding one or more proteins of thepresent invention and/or other proteins). Host cells of the presentinvention either can be endogenously (i.e., naturally) capable ofproducing mite Group 1 proteins of the present invention or can becapable of producing such proteins after being transformed with at leastone nucleic acid molecule of the present invention. Host cells of thepresent invention can be any cell capable of producing at least oneprotein of the present invention, and include bacterial, fungal(including yeast), parasite (including helminth, protozoa andectoparasite), other insect, other animal and plant cells. Examples ofhost cells and transcription control sequences to be used in expressionof such nucleic acid molecules include, but are not limited to, thosedisclosed in U.S. patent application Ser. No. 09/292,225, filed Apr. 15,1999, by McCall et al (U.S. patent application Ser. No. 09/292,225);U.S. patent application Ser. No. 09/292,225, ibid., is incorporated byreference herein in its entirety. Preferred host cells and transcriptioncontrol sequences include bacterial and yeast cells and controlsequences, with E. coli and methyltrophic yeast, and particularly thosemethyltrophic yeast genera and species disclosed herein, being morepreferred.

Another embodiment of the present invention is an isolated proteinhaving the amino acid sequence SEQ ID NO:38 and/or SEQ ID NO:41. Thepresent invention also includes nucleic acid molecules encoding suchproteins, as well as recombinant molecules and recombinant cellscomprising such nucleic acid molecules.

One embodiment of the present invention is a method to detect miteallergy in an animal, which includes the steps of: (a) contacting anisolated mite Group 1 protein produced in accordance with the presentinvention with a putative IgE-containing substance under conditionssuitable to form a complex between the mite group 1 protein and IgE(i.e., a mite Group 1 protein:IgE complex); and (b) determining thepresence of IgE reactive with the mite Group 1 protein by detecting thecomplex, wherein presence of reactive IgE is indicative of mite allergyin the animal. Presence of such a mite Group 1 protein:IgE complex (i.e.a complex between IgE and a mite Group 1 protein of the presentinvention) indicates that the animal is producing IgE reactive with miteGroup 1 protein and, as such, the animal is suffering from mite allergyor is susceptible to mite allergy. Preferred IgE to detect using a miteGroup 1 protein include any mammalian IgE, with human IgE, canine IgE,feline IgE, equine IgE, murine IgE and rat IgE being more preferred,with human and canine IgE being particularly preferred.

Animals in which to detect IgE include mammals and birds, with humans,dogs, cats, horses and other pets, work and/or economic food animalsbeing preferred. Particularly preferred animals in which to detect IgEare humans and dogs. As used herein, canine refers to any member of thedog family, including domestic dogs, wild dogs and zoo dogs. Examples ofdogs include, but are not limited to, domestic dogs, wild dogs, foxes,wolves, jackals and coyotes. As used herein, feline refers to any memberof the cat family, including domestic cats, wild cats and zoo cats.Examples of cats include, but are not limited to, domestic cats, wildcats, lions, tigers, leopards, panthers, cougars, bobcats, lynx,jaguars, cheetahs, and servals. As used herein, equine refers to anymember of the horse family, including, but are not limited to, domestichorses, wild horses and zoo horses.

As used herein, the term “contacting” refers to combining or mixing, inthis case a putative IgE-containing substance with a mite Group 1protein. Formation of a complex between a mite Group 1 protein and anIgE refers to the ability of the mite Group 1 protein to selectivelybind to the IgE in order to form a stable complex that can be measured(i.e., detected, determined). As used herein, the term selectively bindsto an IgE refers to the ability of a mite Group 1 protein of the presentinvention to preferentially bind to IgE, without being able tosubstantially bind to other antibody isotypes. Binding between a miteGroup 1 protein and an IgE is effected under conditions suitable to forma complex; such conditions (e.g., appropriate concentrations, buffers,temperatures, reaction times) as well as methods to optimize suchconditions are known to those skilled in the art, and examples aredisclosed herein. Examples of complex formation conditions are alsodisclosed in, for example, Sambrook et al., ibid. Examples ofimmunological assays are disclosed in, for example, Price, C. andNewman, D., eds, Principles and Practice of Immunoassay, 2nd Edition,(1997) Stockton Press, New York, N.Y., which is incorporated byreference herein in its entirety.

As used herein, the term detecting complex formation refers todetermining if any complex is formed, i.e., assaying for the presence(i.e., existence) of a complex. If complexes are formed, the amount ofcomplexes formed can, but need not be, determined. Complex formation, orselective binding, between mite Group 1 protein and any IgE in thesubstance can be measured (i.e., detected, determined) using a varietyof methods standard in the art (see, for example, Sambrook et al.ibid.), examples of which are disclosed herein.

As used herein a putative IgE-containing substance is any material inwhich IgE antibodies may exist. In one embodiment, a putativeIgE-containing substance of the present invention includes a biologicalsample from an animal. A suitable biological sample includes, but is notlimited to, a bodily fluid substance or a cellular substance. A bodilyfluid refers to any fluid that can be collected (i.e., obtained) from ananimal, examples of which include, but are not limited to, blood, serum,plasma, urine, tears, aqueous humor, cerebrospinal fluid (CSF), saliva,lymph, nasal secretions, tracheobronchial aspirates, milk, feces andfluids obtained through bronchial alveolar lavage. Such a IgE-containingsubstance of the present invention can, but need not be, pretreated toremove at least some of the non-IgE isotypes of immunoglobulin and/orother proteins, such as albumin, present in the fluid. Such removal caninclude, but is not limited to, contacting the bodily fluid with amaterial, such as Protein G, to remove IgG antibodies and/or affinitypurifying IgE antibodies from other components of the body fluid byexposing the fluid to, for example, Concanavalin A. In anotherembodiment, a substance includes collected bodily fluid that ispretreated to concentrate immunoglobulin contained in the fluid. Forexample, immunoglobulin contained in a bodily fluid can be precipitatedfrom other proteins using ammonium sulfate. A preferred IgE-containingsubstance of the present invention is serum.

A complex can be detected in a variety of ways including, but notlimited to use of one or more of the following assays: an enzyme-linkedimmunoassay, a radioimmunoassay, a fluorescence immunoassay, achemiluminescent or other luminescent assay, a lateral flow assay, aflow-through assay, an agglutination assay, a particulate-based assay(e.g., using particulates such as, but not limited to, magneticparticles or plastic polymers, such as latex or polystyrene beads), animmunoprecipitation assay, a BioCore™ assay (e.g., using colloidal gold)and an immunoblotting assay (e.g., a western blot). Such assays are wellknown to those skilled in the art. Assays can be used to givequalitative or quantitative results depending on how they are used. Someassays, such as agglutination, particulate separation, andimmunoprecipitation, can be observed visually (e.g., either by eye or bya machines, such as a densitometer or spectrophotometer) without theneed for a detectable marker. In other assays, conjugation (i.e.,attachment) of a detectable marker to a mite Group 1 protein or to amolecule that selectively binds to the IgE being detected aids indetecting complex formation. Examples of detectable markers include, butare not limited to, a radioactive label, a fluorescent label, achemiluminescent or other luminescent label, a chromophoric label or aligand. A ligand refers to a molecule that binds selectively to anothermolecule. Preferred detectable markers include, but are not limited to,fluorescein, a radioisotope, a phosphatase (e.g., alkaline phosphatase),biotin, avidin, a peroxidase (e.g., horseradish peroxidase), aluciferase, and biotin-related compounds or avidin-related compounds(e.g., streptavidin or ImmunoPure® NeutrAvidin).

In one embodiment a complex can be formed and detected in solution. Inanother embodiment, a complex can be formed in which one or more membersof the complex are immobilized on (e.g., coated onto) a supportsubstrate. Immobilization techniques are known to those skilled in theart. Suitable support substrate materials include, but are not limitedto, plastic, glass, gel, celluloid, paper, PVDF(poly-vinylidene-fluoride), nylon, nitrocellulose, and particulatematerials such as latex, polystyrene, nylon, nitrocellulose, agarose andmagnetic resin. Suitable shapes for support substrate material include,but are not limited to, a well (e.g., microtiter dish well), a plate, adipstick, a bead, a lateral flow apparatus, a flow-through apparatus, amembrane, a filter, a tube, a dish, a celluloid-type matrix, a magneticparticle, and other particulates. A particularly preferred supportsubstrate comprises an ELISA plate, a dipstick, a radioimmunoassayplate, agarose beads, plastic beads, latex beads, immunoblot membranesand immunoblot papers. In one embodiment, a support substrate, such as aparticulate, can include a detectable marker.

A preferred method to detect IgE is an immunosorbent assay. Animmunoabsorbent assay of the present invention comprises a capturemolecule and an indicator molecule. A capture molecule of the presentinvention binds to an IgE in such a manner that the IgE is immobilizedto a support substrate. As such, a capture molecule is preferablyimmobilized to a support substrate of the present invention prior toexposure of the capture molecule to a putative IgE-containing substance.As such, an indicator molecule preferably is not immobilized to the samesupport substrate as a capture molecule prior to exposure of the capturemolecule to a putative IgE-containing substance.

In one embodiment, a mite Group 1 protein of the present invention, alsoreferred to as a mite Group 1 antigen or allergen of the presentinvention, is used as a capture molecule by being immobilized on asupport substrate, such as a microtiter dish well or a dipstick. Abiological sample collected from an animal is applied to the supportsubstrate and incubated under conditions suitable (i.e., sufficient) toallow for antigen:IgE complex formation bound to the support substrate(i.e., IgE in a sample binds to a mite Group 1 protein immobilized on asupport substrate). Excess non-bound material (i.e., material from thebiological sample that has not bound to the antigen), if any, is removedfrom the support substrate under conditions that retain antigen:IgEcomplex binding to the support substrate. Preferred conditions aregenerally disclosed in Sambrook et al., ibid. A detection molecule isadded and incubated to allow formation of a complex between thedetection molecule and the antigen:IgE complex. Excess detectionmolecule is removed, a developing agent is added if required, and thecomplex is submitted to a detection device for analysis. A preferreddetection molecule for this embodiment is an IgE-binding molecule, suchas an anti-IgE isotype or idiotype antibody, or other molecule thatselectively binds IgE, for example an IgE receptor (FcJ2) protein oralpha chain protein thereof, examples of which are described in, forexample, U.S. Pat. No. 5,945,294, issued Aug. 31, 1999, by Frank et al.(U.S. Pat. No. 5,945,294); U.S. Pat. No. 5,958,880, issued Sep. 28,1999, by Frank et al. (U.S. Pat. No. 5,958,880); PCT Patent PublicationNo. WO 98/45707, published Oct. 15, 1998, by Frank et al. (WO 98/45707);PCT Patent Publication No. WO 99/38974, published Aug. 5, 1999, by Weberet al. (WO 99/38974); and U.S. patent application Ser. No. 09/287,380,filed Apr. 6, 1999, by deWeck et al. (U.S. patent application Ser. No.09/287,380); each of these issued patents, patent applications, andpatent publications is incorporated by reference herein in its entirety.A detection molecule is preferably conjugated to a detectable markersuch as those disclosed herein. Also included in the present inventionis the use of multiple reagents to amplify a signal, such as secondaryor tertiary antibodies or other binding molecules.

In one embodiment, an anti-IgE antibody (e.g., isotype or idiotypespecific antibody) is used as a capture molecule by being immobilized ona support substrate, such as a microtiter dish well or a dipstick. Abiological sample collected from an animal is applied to the supportsubstrate and incubated under conditions suitable to allow for anti-IgEantibody:IgE complex formation bound to the support substrate. Excessnon-bound material, if any, is removed from the support substrate underconditions that retain anti-IgE antibody:IgE complex binding to thesupport substrate. A mite Group 1 protein is added to the supportsubstrate and incubated to allow formation of a complex between the miteGroup 1 protein and the anti-IgE antibody:IgE complex. Preferably, themite Group 1 protein is conjugated to a detectable marker such as thosedisclosed herein. Excess mite Group 1 protein is removed, a developingagent is added if required, and the sample is submitted to a detectiondevice for analysis. One or more antibody layers can also be used todetect mite Group 1 protein binding.

In one embodiment, an immunosorbent assay of the present invention doesnot utilize a capture molecule. In this embodiment, a biological samplecollected from an animal is applied to a support substrate, such as amicrotiter dish well or a dipstick, and incubated under conditionssuitable to allow for IgE binding to the support substrate. Any IgEpresent in the bodily fluid is immobilized on the support substrate.Excess non-bound material, if any, is removed from the support substrateunder conditions that retain IgE binding to the support substrate. Amite Group 1 protein is added to the support substrate and incubated toallow formation of a complex between the mite Group 1 protein and theIgE. Preferably, the mite Group 1 protein is conjugated to a detectablemarker. Excess mite Group 1 protein is removed, a developing agent isadded if required, and the sample is submitted to a detection device foranalysis.

Another preferred method to detect IgE is a lateral flow assay, examplesof which are disclosed in U.S. Pat. No. 5,424,193, issued Jun. 13, 1995,by Pronovost et al.; U.S. Pat. No. 5,415,994, issued May 16, 1995, byImrich et al; WO 94/29696, published Dec. 22, 1994, by Miller et al.;and WO 94/01775, published Jan. 20, 1994, by Pawlak et al.; each ofthese patent publications is incorporated by reference herein in itsentirety. In one embodiment, a biological sample is placed in a lateralflow apparatus that includes the following components: (a) a supportstructure defining a flow path; and (b) a labeling reagent comprising alabeled (e.g., colored) bead conjugated to a mite Group 1 protein of thepresent invention, the labeling reagent being impregnated within thesupport structure in a labeling zone; and (c) a capture reagentcomprising an IgE-binding molecule, such as an anti-IgE antibody or anIgE receptor protein or alpha chain protein thereof. Preferred miteGroup 1 proteins include those disclosed herein. It is to be noted thatin another embodiment, the labeling reagent include an IgE-bindingmolecule and the capture reagent can be a mite Group 1 protein of thepresent invention. In either embodiment, the capture reagent is locateddownstream of the labeling reagent within a capture zone fluidlyconnected to the labeling zone in such a manner that the labelingreagent can flow from the labeling zone into the capture zone. Thesupport structure defines a flow path that is lateral and includes acapture zone. The apparatus can further comprise a sample receiving zonelocated along the flow path, more preferably upstream of the capturereagent. The flow path in the support structure is created by contactinga portion of the support structure downstream of the capture zone,preferably at the end of the flow path, to an absorbent capable ofabsorbing excess liquid.

Another preferred method to detect IgE is a flow through assay, examplesof which are disclosed in U.S. Pat. No. 4,727,019, issued Feb. 23, 1988,by Valkirs et al, which is incorporated by reference in its entirety. Inone embodiment, a biological sample is placed in a flow throughapparatus that includes the following components: (a) a porous solidphase having lower and upper surfaces arranged so that the biologicalsample is applied to the upper surface, the upper surface also includinga test area that includes a capture reagent; and (b) an absorbent phasecontacting the lower surface of the solid that collects liquid from thebiological sample that has permeated the solid phase. The capturereagent can be either a mite Group 1 protein of the present invention oran IgE-binding molecule. After the sample flows through the apparatus, adetection reagent is added to the apparatus such that any captured IgEcan be detected. Examples of detection reagents include (a) a mite Group1 protein of the present invention, which is used when the capturereagent used is an IgE-binding molecule and (b) an IgE-binding molecule,which is used when the capture reagent used is a mite Group 1 protein.Detection is accomplished using means known to those skilled in the art.

The present invention also includes a kit to detect mite allergy in ananimal, based on each of the disclosed detection methods. Suitable andpreferred mite Group 1 proteins are disclosed herein. One embodiment isa kit to detect IgE specific for mite Group 1 proteins comprising a miteGroup 1 protein and a means for detecting an IgE antibody thatselectively binds to a mite Group 1 protein. Suitable means of detectioninclude compounds disclosed herein that bind to either the mite Group 1protein, such as an anti-mite Group 1 protein antibody, or to IgE, suchas an antibody that selectively bind to IgE (an anti-IgE antibody) or anIgE receptor protein or alpha chain protein thereof. In one embodiment,a kit also includes one or more additional antigens to determine if ananimal is susceptible to or suffers from allergy to such antigen(s).Examples of such allergens include, but are not limited to, thosedisclosed in U.S. Pat. No. 5,945,294, ibid.; U.S. Pat. No. 5,958,880,ibid.; WO 98/45707, ibid.; WO 99/38974, ibid.; and U.S. patentapplication Ser. No. 09/287,380, ibid.

Additional teachings with respect to methods and kits to detect allergyto Group 1 proteins can be found, for example, in U.S. Pat. No.5,646,115, issued Jul. 8, 1997, by Frank et al. (U.S. Pat. No.5,646,115); U.S. Pat. No. 5,840,695, issued Nov. 24, 1998, by Frank etal. (U.S. Pat. No. 5,840,695); U.S. Pat. No. 5,932,470, issued Aug. 3,1999, by Frank et al. (U.S. Pat. No. 5,932,470); U.S. Pat. No.5,945,294, ibid.; U.S. Pat. No. 5,958,880, ibid.; WO 98/45707, ibid.; WO99/38974, ibid.; and U.S. patent application Ser. No. 09/287,380, ibid.U.S. Pat. No. 5,646,115, ibid., U.S. Pat. No. 5,840,695, ibid., and U.S.Pat. No. 5,932,470 are each incorporated by reference herein in itsentirety.

One embodiment of the present invention is a composition that, whenadministered to an animal in an effective manner, is capable of reducingan allergic response to a mite Group 1 protein in a mite Group 1 proteinallergic animal. Such a composition can function as a preventative, orprophylactic, or as a therapeutic, or treatment. Such a compositionincludes an isolated mite Group 1 protein of the present invention andat least one of the following components: an excipient, an adjuvant, anda carrier that the animal can tolerate. Examples of excipients,adjuvants and carriers are found throughout the art; see, for example,U.S. Pat. No. 5,958,880, ibid. and 5,840,695, ibid.

In one embodiment, a mite Group 1 protein of the present invention canbe genetically engineered or otherwise altered to lessen or completelyabolish a mite Group 1 protein's ability to bind to IgE. Such amolecule, referred to herein as a mite Group 1 protein of the presentinvention with reduced IgE reactivity, can be used to reduce an animal'sallergic response to exposure to a mite Group 1 protein.

Suitable protocols by which to administer compositions of the presentinvention in an effective manner can vary according to individual dosesize, number of doses, frequency of dose administration, and mode ofadministration. Determination of such protocols can be accomplished bythose skilled in the art. An effective dose refers to a dose capable oftreating an animal against hypersensitivity to mite allergens. Effectivedoses can vary depending upon, for example, the composition used and thesize and type of the recipient animal, i.e. what species. Effectivedoses to immunomodulate an animal against a mite Group 1 protein includedoses administered over time that are capable of alleviating ahypersensitive response by an animal to a mite Group 1 protein. Forexample, a first tolerizing dose can comprise an amount of a compositionof the present invention that causes a minimal hypersensitive responsewhen administered to a hypersensitive animal. A second tolerizing dosecan comprise a greater amount of the same composition than the firstdose. Effective tolerizing doses can comprise increasing concentrationsof the composition necessary to tolerize an animal such that the animaldoes not have a hypersensitive response to exposure to a mite Group 1protein. An effective dose to desensitize an animal can comprise aconcentration of a composition of the present invention sufficient toblock an animal from having a hypersensitive response to exposure to amite allergen present in the environment of the animal. Effectivedesensitizing doses can include repeated doses having concentrations ofa composition that cause a minimal hypersensitive response whenadministered to a hypersensitive animal.

A suitable single dose is a dose that is capable of treating an animalagainst hypersensitivity to a mite Group 1 protein when administered oneor more times over a suitable time period. For example, a preferredsingle dose of a mite Group 1 protein-containing composition is fromabout 0.5 nanograms (ng) to about 1 gram (g) of the protein per kilogrambody weight of the animal. Further treatments with the composition canbe administered from about 1 day to 1 year after the originaladministration. Further treatments with the composition preferably areadministered when the animal is no longer protected from hypersensitiveresponses to mite Group 1 proteins. Particular administration doses andschedules can be developed by one of the skill in the art based upon theparameters discussed above. Modes of administration can include, but arenot limited to, subcutaneous, intradermal, intravenous, nasal, oral,transdermal and intramuscular routes.

A composition of the present invention can be used in conjunction withother compounds capable of modifying an animal's hypersensitivity tomite allergens. For example, an animal can be treated with compoundscapable of modifying the function of a cell involved in a hypersensitiveresponse, compounds that reduce allergic reactions, such as by systemicagents or anti-inflammatory reagents (e.g. anti-histamines, anti-steroidreagents, anti-inflammatory reagents and reagents that driveimmunoglobulin heavy chain class switching from IgE to IgG). Suitablecompounds useful for modifying the function of a cell involved in ahypersensitive response include, but are not limited to, antihistamines,cromolyn sodium, theophylline, cyclosporin A, adrenalin, cortisone,compounds capable of regulating cellular signal transduction, compoundscapable of regulating adenosine 3′, 5′ cyclic phosphate (cAMP) activity,and compounds that block IgE activity, such as peptides from IgE or IgEspecific Fc receptors, antibodies specific for peptides from IgE orIgE-specific Fc receptors, or antibodies capable of blocking binding ofIgE to Fc receptors.

A composition of the present invention can also be used in conjunctionwith other antigens to prevent or treat allergic, infectious, or otherdiseases. Examples of antigens causing allergy include, but are notlimited to those disclosed in U.S. Pat. No. 5,945,294, ibid.; U.S. Pat.No. 5,958,880, ibid.; WO 98/45707, ibid.; WO 99/38974, ibid.; and U.S.patent application Ser. No. 09/287,380, ibid.

Additional teachings with respect to compositions and uses thereof toreduce allergy can be found, for example, in U.S. Pat. No. 5,958,880,ibid. and 5,840,695, ibid.

The following examples are provided for the purposes of illustration andare not intended to limit the scope of the present invention. Thefollowing examples include a number of recombinant DNA and proteinchemistry techniques known to those skilled in the art; see, forexample, Sambrook et al., ibid.

EXAMPLES Example 1

This Example describes the production of certain novel mite Group 1nucleic acid molecules and proteins of the present invention. ThisExample also describes expression of such nucleic acid molecules andproteins by recombinant Pichia microorganisms of the present invention.

A. This example describes the production and expression in Pichia of aDer f 1 Group 1 cDNA nucleic acid molecule, denoted herein asnDerf1_(909b), the coding strand of which, represented by SEQ ID NO:28,incorporates Pichia-preferred codon changes as compared tonDerf1_(909a), having a coding strand nucleic acid sequence of SEQ IDNO:4. Nucleic acid molecule nDerf1_(909b) encodes a pro-form of a Der f1 Group 1 protein, namely PDerf1_(303b). The following codon changeswere made to produce nDerf1_(909b) from nDerf1_(909a): a change from CGAto AGA in the codon spanning nucleotide positions 538 to 540 of SEQ IDNO:4; a change from CGA to AGA in the codon spanning nucleotidepositions 547 to 549 of SEQ ID NO:4; a change from CGA to AGA in thecodon spanning nucleotide positions 553 to 555 of SEQ ID NO:4; and achange from CGA to AGA in the codon spanning nucleotide positions 556 to558 of SEQ ID NO:4. Translation of the resultant coding strand havingSEQ ID NO:28 yielded SEQ ID NO:29, also represented as PDerf1_(303b).SEQ ID NO:30 represents the reverse complement of SEQ ID NO:28, i.e.,the complementary strand of nDerf1_(909b).

Specifically, nucleic acid molecule nDerf1_(909b) was produced asfollows. Two sets of two primers each were designed to allow forselective optimization of four closely situated arginine codons and toprovide a signal peptide (the S. cerevisiae alpha factor) codingsequence for efficient secretion of the expressed protein from P.pastoris. The first set of two primers, the first being sense primer 5′CGC GTC CCT CTC GAG AAA AGA GAG GCT AGA CCA GCT TCA ATC AAA 3′ (SEQ IDNO:46) and the second being the antisense primer 5′ GGG CTT TCC TTT TGCGGC CGC TCA CAT GAT TAC AAC ATA TGG 3′ (SEQ ID NO:47), incorporate XhoIand NotI cloning sites (shown in bold) to facilitate cloning into an E.coli/P. pastoris shuttle plasmid, pPICZalphaB (available from InvitrogenCorp., Carlsbad, Calif.), such that the Der f 1 nucleic acid moleculewould be operatively linked to the P. pastoris AOX promoter. Primer SEQID NO:46 was constructed to join nucleotides encoding the followingamino acid segments: the C-terminal portion of the S. cerevisiae alphapeptide (LEU-GLU), the KEX2 cleavage site (LYS-ARG), and a GLU-ALAspacer sequence to the first residue (ARG) of the Der f 1 pro-protein.The second set of primers, the first being sense primer 5′ GCA AGA GAACAA AGA TGC AGA AGA CCA AAT TCG C 3′ (SEQ ID NO:48), and the secondbeing 5′ GCG AAT TTG GTC TTC TGC ATC TTT GTT CTC TTG C 3′ (SEQ IDNO:49), overlap on opposite strands of the nucleotide sequence for SEQID NO:4 and change CGA, an infrequently used arginine codon for yeast,to AGA, the most abundant codon for this residue. The changed codons forSEQ ID NO:48 are in bold. The approximately 950-nucleotide PCR productwas generated by a three step process. In the first step, primers SEQ IDNO:46 and SEQ ID NO:49 were combined with a D. farinae cDNA libraryprepared as described in U.S. patent application Ser. No. 09/292,225,ibid., to produce an approximately 600-nucleotide fragment. The PCRreaction included the following reactants in a 50 microliter (21)reaction volume: 2 μl D. farinae cDNA library, 1×PFU polymerase buffer(available from Stratagene, LaJolla, Calif.), 0.2 mM each of the fourdNTPs and 2.5 Units PFU polymerase (all available from Stratagene), 0.5micromolar (μM) of the primers having SEQ ID NO:46 and SEQ ID NO:49.Amplification conditions were as follows: 1 cycle of 96° C. for 3minutes, then 30 cycles of the following: 96° C. for 1 minute, 55° C.for 1 minute, 72° C. for 2 minutes; followed by 1 cycle of 72° C. for 7minutes. A second PCR reaction, using the aforementioned conditions andprimers having SEQ ID NO:48 and SEQ ID NO:47, was performed resulting inan approximately 400-nucleotide product. The two PCR products were gelpurified, annealed together to form a template for a third round of PCRusing the conditions specified previously. The resulting approximately900-nucleotide product was gel purified, digested with XhoI and NotI,ligated into similarly digested pPICZalphaB, and transformed into E.coli strain DH5alpha to create plasmid pBC128, also referred to hereinas recombinant molecule pBC128. The plasmid was linearized at a uniqueSacI site and introduced into P. pastoris strain X33 by electroporationas described by Guarente et al., 1991 Methods Enzymol 194, 182-187.Recombinant cells resistant to 1 milligram/milliliter (mg/ml) zeocin,presumed to have multiple integrated copies of the linearized plasmidpBC128, were selected. Integration of the expression cassette into theP. pastoris genome was confirmed by PCR. Expression, using techniquesknown to those skilled in the art, of representative zeocin-resistantrecombinant P. pastoris microorganisms were evaluated after inductionwith methanol for two days. One recombinant cell, denoted P. pastorisHCY215, was found to express relatively high levels of a protein of theappropriate molecular weight by sodium dodecyl sulfate (SDS)polyacrylamide gel electrophoresis (PAGE) and silver staining, usingmethods known in the art.

B. This example describes the production and expression in Pichia of aDer f 1 Group 1 cDNA nucleic acid molecule, denoted herein asnDerf1_(669b), the coding strand of which, represented by SEQ ID NO:31,incorporates Pichia-preferred codon changes as compared tonDerf1_(669a), having a coding strand nucleic acid sequence of SEQ IDNO:7. Nucleic acid molecule nDerf1_(669b) encodes a mature form of a Derf 1 Group 1 protein, namely PDerf1_(223b), represented by SEQ ID NO:32.SEQ ID NO:33 represents the complementary strand of nucleic acidmolecule nDerf1_(669b).

An expression plasmid encoding the mature form of Der f 1 with codonsaltered for optimized expression in P. pastoris was produced usingrecombinant molecule pBC128 (produced as described in Example 1A) astemplate. pBC128 was submitted to PCR mutagenesis using primers SB11(sense primer with nucleic acid sequence CGC ATA GTC CCT CTC GAG AAA AGAACA AGC GCT TGC CGT ATC, SEQ ID NO:54) and the primer with SEQ ID NO:47.Primer SEQ ID NO:54 incorporates a 5-prime XhoI restriction site (shownin bold) and fuses the first codon of nDerf1_(669b) in frame with thenucleic acid sequence encoding the KEX2 cleavage site (LYS-ARG) ofpPICZAlphaA. A single round of PCR amplification was performed in a50-μl reaction volume using conditions as described in Example 1A with50 ng of plasmid pBC128 (containing nDerf1_(909b), the coding strand ofwhich is represented by SEQ ID NO:28) as template and primers SEQ IDNO:54 and SEQ ID NO:47. The PCR product, denoted herein as plasmidpBC138, or recombinant molecule pBC138, is identical to pBC128 exceptthat pBC138 contains nDerf1_(669b) instead of nDerf1_(909b) and, assuch, lacks nucleic acid sequences encoding the 80-residue “pro” peptideof Der f 1. The specific codon changes in nDerf1_(669b) (with a codingstrand nucleic acid sequence of SEQ ID NO:31) as compared tonDerf1_(669a) (with a coding strand nucleic acid sequence of SEQ IDNO:7) which encodes a wild-type D. farinae mature-form Group 1 protein,are as follows: changes from CGA to AGA in the codons spanningnucleotide positions (a) 298 to 300, (b) 307 to 309, (c) 313 to 315, and(d) 316-318 of SEQ ID NO:7. Recombinant molecule pBC138 was linearizedwith SacI, electroporated into competent P. pastoris strain X33 cells,and a zeocin-resistant recombinant cell, denoted herein as HCY286 wasselected as described in Example 1A.

C. This example describes the production and expression in Pichia of aDer f 1 Group 1 cDNA nucleic acid molecule, denoted herein asnDerf1_(909d), the coding strand of which, represented by SEQ ID NO:37,incorporates Pichia-preferred codon optimization changes as well as acodon change that removes an N-glycosylation site, as compared tonDerf1_(909a), having a coding strand nucleic acid sequence of SEQ IDNO:4. The Der f 1 pro-form protein PDerf1_(303a) (SEQ ID NO:5) containsa single N-glycosylation site (NTS) at residues 133-135 of SEQ ID NO:5.An expression plasmid encoding a non-glycosylated pro-form of Der f 1with codons altered for optimized expression in P. pastoris was producedby inverse mutagenesis using recombinant molecule pBC128 (produced asdescribed in Example 1A) containing nucleic acid molecule nDerf1_(909b)as template. The resulting recombinant molecule contained the mutatednucleic acid molecule nDerf1_(909d), a Der f 1 nucleic acid molecule inwhich the codon encoding asparagine (AAC) spanning nucleotides 397 to399 of SEQ ID NO:28 was altered to encode glutamine (CAA) at the samepositions in SEQ ID NO:37. Nucleic acid molecule nDerf1_(909d) encodes apro-form of a Der f 1 Group 1 protein lacking any N-glycosylation sites,namely PDerf1_(303d), represented by SEQ ID NO:38. SEQ ID NO:39represents the complementary strand of nucleic acid moleculenDerf1_(909d).

The PCR reaction included the following components in a 50-pd reactionvolume: 25 ng nDerf1_(909b)-containing plasmid pBC128, 1×PFU polymerasebuffer, 0.2 mM each of the four dNTPs, 2.5 U PFU polymerase, 0.5 μMprimer SEQ ID NO:57 and SEQ ID NO:58. Primers SEQ ID NO:57 (sense primercorresponding to nucleotides (5′ GCCGCAACTG AATCAGCTTA TTTGGCCTACCGTCAAACGT CTTTGG 3′) and SEQ ID NO:58 (antisense primer correspondingto nucleotides 5′ GACACCAGAG AAAGCCCAAC ATGAACCACA GCCTCCTTGC ATACG 3′)contain 5-prime phosphates and are situated end-to-end on oppositestrands of the DNA template. Primer SEQ ID NO:57 changes an asparaginecodon (AAC) to glutamine (CAA); the relevant nucleotides are shown inbold in the above primer sequence. The amplification conditions were: 1cycle of 96° C. for 3 min, 30 cycles of 96° C. for 1 min, 55° C. for 1min, 72° C. for 9 min, and 1 cycle of 72° C. for 7 min. The amplifiedproduct was desalted and self-ligated to form recombinant moleculepBC158, which contains nDerf1_(909d), the coding strand of which isrepresented by SEQ ID NO:37. Recombinant molecule pBC158 was linearizedwith SacI, electroporated into competent P. pastoris strain X33 cells,and a zeocin-resistant recombinant cell, denoted herein as HCY288 wasselected as described in Example 1A. Expression of recombinant cellHCY288 under conditions as described in Example 1A yieldedPDerf1_(303d), which when submitted to SDS-PAGE migrated in a mannersimilar to that of a non-glycosylated protein.

D. This example describes the production and expression in Pichia of aDer f 1 Group 1 cDNA nucleic acid molecule, denoted herein asnDerf1_(669c), the coding strand of which, represented by SEQ ID NO:40,incorporates Pichia-preferred codon optimization changes as well as acodon change that removes an N-glycosylation site, as compared tonDerf1_(669a), having a coding strand nucleic acid sequence of SEQ IDNO:7. The Der f 1 mature protein PDerf1_(223a) (SEQ ID NO:8) contains asingle glycosylation site (NTS) at residues 53-55 of SEQ ID NO:8. Anexpression plasmid encoding a non-glycosylated mature form of Der f 1with codons altered for optimized expression in P. pastoris is producedfrom recombinant molecule pBC158, produced as described in Example 1C,using a strategy as described in Example 1B. That is, pBC158 issubmitted to PCR amplification in the presence of primers having SEQ IDNO:47 and SEQ ID NO:54 under conditions as described in Example 1B. Theresultant recombinant molecule, denoted herein as pBC168, containsmutated nucleic acid molecule nDerf1_(669c), a Der f 1 nucleic acidmolecule in which the codon corresponding to that encoding asparagine(AAC) spanning nucleotides 397 to 399 of SEQ ID NO:28 is altered toencode glutamine (CAA) in SEQ ID NO:40. As such, nucleic acid moleculenDerf1₆₆₉, encodes a mature form of a Der f 1 Group 1 protein lackingany N-glycosylation sites, namely PDerf1_(223d), represented by SEQ IDNO:41. SEQ ID NO:41 has a Q rather than N at amino acid residue 53. SEQID NO:42 represents the complementary strand of nucleic acid moleculenDerf1_(669a).

Recombinant molecule pBC168 is linearized with SacI, electroporated intocompetent P. pastoris strain X33 cells, and a zeocin-resistantrecombinant cell selected as described in Example 1A.

Example 2

This Example describes the expression and purification of certainrecombinant mite Group 1 proteins of the present invention fromsupernatant cultures of recombinant Pichia microorganisms.

Recombinant P. pastoris microorganisms, also denoted herein as strains,were routinely cultured on YPD culture medium (1% yeast extract, 2%peptone, 2% dextrose). His+ transformants were selected on MD culturemedium (1.34% yeast nitrogen base, 0.00004% biotin, 2% dextrose).Small-scale inductions of expression of recombinant P. pastoris strainscontaining Derf1 nucleic acid molecules were performed using BMG or BMMculture media which were composed of the following: 100 mM potassiumphosphate, pH6.0, 1.34% yeast nitrogen base, 0.00005% biotin and either1% glycerol (BMG) or 0.5% methanol (BMM). For each recombinant straingrown and induced, a single colony of that strain was inoculated into 25ml BMG culture medium in a 250 ml baffled flask covered with a poroussilicon rubber stopper to allow maximum aeration. The culture was grownat 28° C. with shaking to an optical density (A600) of about 1.0. Theculture was then pelleted for 10 min at 3000×g (times gravity) andresuspended in 250 ml BMM culture medium at an optical density (A600) ofabout 1.0 in a 2-liter (L) baffled flask with a porous silicon rubberstopper to induce expression of a Der f 1 nucleic acid moleculeoperatively linked to the AOX promoter. The culture was incubated at 28°C. for 4 days; methanol was added daily to a final concentration of 0.5%volume/volume (v/v). The entire culture volume was concentrated to 20%of original volume by tangential flow filtration (3000 MW cutoff,available from AG Technologies Needham, Mass.) and analyzed by SDS-PAGE.

The supernatant from the culture was recovered and diluted 1:3 (v/v)with 25 mM sodium acetate pH 4.5 (Buffer A) and loaded onto a 1.6×10 mmSP-Sepharose (available from Amersham-Pharmacia Biotech, Piscataway,N.J.) previously equilibrated with 25 mM sodium acetate, pH 4.5. Boundprotein was eluted with a linear salt gradient to 100% Buffer B (25 mMsodium acetate, 1 M NaCl, pH 4.5) in 20 to 25 column volumes. Fractions(5.0 ml) were collected and analyzed by SDS-PAGE and reverse phase RPC18chromatography. Recombinant Der f 1 proteins produced by recombinant P.pastoris microorganisms eluted at 0.1 to 0.15 M NaCl and migrated as adiffuse band with an apparent molecular weight ranging from about 40 to46 kD. Fractions containing Der f 1 proteins (>90% homogeneous) werepooled and concentrated using a 10-kd) molecular weight cut-off (MWCO)centriprep concentrator.

The Der f 1 protein expressed by recombinant cell P. pastoris HCY215 (P.pastoris strain X33 transformed with plasmid pBC128 containing nucleicacid molecule nDerf1_(909b) (coding strand of SEQ ID NO:28) whichencodes the pro-form of Der f 1 (amino acid sequence SEQ ID NO:29)),produced as described in Example 1A, was subjected to N-terminalsequence analysis, using methods known in the art. The N-terminalsequence obtained was analyzed and was found to consist of a mixture oftwo sequences, with the first being AETSACRINS VNVPSELDLR SLR-, denotedSEQ ID NO:55, and the second being TSACRINSVN VPSELDLRSL R—, denoted SEQID NO:56. The sequences obtained surprisingly represent the N-terminusof mature form of the Der f protein, which indicates that P. pastoris isable to express the Der f 1 pro-form and cleave it to produce the matureDer f 1 protein. Since two sequences were obtained, with the firstsequence having two extra residues on the N-terminus, it appears that P.pastoris cleaves the pro-protein PDerf1_(303b) (SEQ ID NO:29) at twolocations: between the asparagine at position 78 and the alanine atposition 79 of SEQ ID NO:29; and between the glutamate at position 80and threonine at position 81 of SEQ ID NO:29, respectively.

Example 3

This Example describes the production of certain novel mite Group 1nucleic acid molecules of the present invention. This Example alsodescribes expression of such nucleic acid molecules by recombinant E.coli microorganisms of the present invention.

A. This example describes the production and expression in E. coli of aDer f 1 Group 1 cDNA nucleic acid molecule, denoted herein as nDerf1₉₀₉₀the coding strand of which, represented by SEQ ID NO:34, incorporates E.coli-preferred codon changes as compared to nDerf1_(909a), having acoding strand nucleic acid sequence of SEQ ID NO:4. Nucleic acidmolecule nDerf1_(909c) encodes a pro-form of a Der f 1 Group 1 protein,namely PDerf1_(303c). The following codon changes were made to producenDerf1_(909c) from nDerf1_(909a): a change from CCA to CCG in the codonspanning nucleotide positions 4 to 6 of SEQ ID NO:4; a change from CGAto CGT in the codon spanning nucleotide positions 547 to 549 of SEQ IDNO:4; a change from CGA to CGT in the codon spanning nucleotidepositions 553 to 555 of SEQ ID NO:4; and a change from CGA to CGT in thecodon spanning nucleotide positions 556 to 558 of SEQ ID NO:4. Inaddition there is a change from TAT to TAC in the codon spanningnucleotide positions 895 to 897 of SEQ ID NO:4 to eliminate a NdeIcloning site within the Der f 1 coding region. Translation of theresultant coding strand having SEQ ID NO:34 yielded SEQ ID NO:35, alsorepresented as PDerf1_(303c). SEQ ID NO:36 represents the reversecomplement of SEQ ID NO:34, i.e., the complementary strand ofnDerf1_(909c).

A PCR mutagenesis strategy similar to the one described in Example 1Awas used to produce nucleic acid molecule nDerf1_(909c). Four primers(SEQ ID NO:50, 51, 52, and 53) were used in a three step PCR process. Inthe first PCR step, an about 600-nucleotide PCR product was generated ina manner as described in the first step of the PCR process described inExample 1A, except that the primers were as follows: the sense primerSEQ ID NO:50, 5′ GGGAGCTCCA TATGCGTCCG GCTTCAATCA AAAACTT 3′ and theantisense primer SEQ ID NO:51, 5′ GCGAATTTGG ACGACGGCAA CGTTGTTCAC 3′.Primer SEQ ID NO:50 incorporates a 5′ NdeI restriction site, shown inbold, and changes codon CCA, a low abundance codon in E. coli, to CCG,the most frequently used codon for that residue; this change isunderlined. Primer SEQ ID NO:51 changes three rare ARG codons from CGA,which is rarely used in E. coli, to CGT, the most frequently used. Inthe second PCR step, an about 370-nucleotide PCR product was generatedin a manner as described in the second step of the PCR process describedin Example 1A, except that the following primers were used: Primer SEQID NO:52, with a sequence of 5′ CCCTCGCGGA TCCTCACATG ATTACAACGT ATGGAT3′ incorporates a restriction site for BamH1 (shown in bold) and changesa TYR codon from TAT to TAC (underlined) to eliminate an NdeI cloningsite within the Der f 1 coding region; Primer SEQ ID NO:53 is a senseprimer with the sequence 5′ GTGAACAACG TTGCCGTCGT CCAAATTCGC 3′. Theapproximately 370-nucleotide PCR fragment generated with SEQ ID NO:53and SEQ ID NO:52, and the approximately 600-nucleotide fragment producedusing primers SEQ ID NO:50 and SEQ ID NO:51, were annealed and theproduct was reamplified with primers SEQ ID NO:50 and SEQ ID NO:53 toproduce an approximately 900-nucleotide fragment which was gel purified,digested with NdeI and BamHI and ligated into similarly cleaved plasmidλPRcro/T2ori/RSET-B, produced as described in PCT Patent Publication No.WO 98/12563, published Mar. 26, 1998, by Grieve et al. The resultingrecombinant molecule, denoted pλPR-nDerf1_(909c), includes nDerf1_(909c)operatively linked to lambda transcription control sequences in order toenable expression of the pro-form of Der f 1 (i.e., PDerf1_(303c)) withan initiating methionine codon for expression in the E. coli.Recombinant molecule pλPR-nDerf1_(909c) was transformed into E. coliHB101 cells to produce recombinant cell (HB101:pλPR-nDerf1_(909c), whichwhen cultured as described in Example 4 leads to production ofrecombinant Der f 1 protein PDerf1_(303c).

B. This example describes the production and expression in E. coli of aDer f 1 Group 1 cDNA nucleic acid molecule, denoted herein asnDerf1_(669d), the coding strand of which, represented by SEQ ID NO:43,incorporates Pichia-preferred codon changes as compared tonDerf1_(669a), having a coding strand nucleic acid sequence of SEQ IDNO:7. Nucleic acid molecule nDerf1_(669d) encodes a mature form of a Derf 1 Group 1 protein, namely PDerf1_(223d), represented by SEQ ID NO:44.SEQ ID NO:45 represents the complementary strand of nucleic acidmolecule nDerf1_(669d).

Nucleic acid molecule nDerf1_(669d) and recombinant moleculepλPR-nDerf1_(669d) are produced using a strategy similar to thatdescribed in Example 1B such that the nucleotides encoding the “pro”region are deleted from nDerf1_(909c) and pλPR-nDerf1_(909c), producedas described in Example 3A. Recombinant molecule pλPR-nDerf1_(669d) istransformed into E. coli HB101 cells to produce recombinant cellHB101:pλPR-nDerf1_(669d), which when cultured as described in Example 4leads to production of recombinant Der f 1 protein PDerf1_(223d).

Example 4

This Example describes the production and purification of a mite Group 1protein of the present invention from E. coli.

Recombinant Der f 1 protein PDerf1_(303c) was produced and purified asfollows. A colony of recombinant cell HB101:pλPR-nDerf1₉₀₉₀ produced asdescribed in Example 3A, was grown in a shake flask at 32° C. in LBbroth containing 100 μg/ml ampicillin to a cell density corresponding toan optical density (A600) of about 0.8 to about 1.0. Expression of Der f1 protein PDerf1_(303c) was induced by shifting the temperature to 42°C. and incubating for an additional 2 to 3 hours. Cells grown in shakeflasks were harvested after chilling to 4° C. by centrifugation at8000×g for 30 minutes in a refrigerated centrifuge (such as Avanti J-20,Beckman Instrument Co., Palo Alto, Calif.) Harvested cells (6 g from 2 Lof cell culture) were suspended in 60 ml breaking buffer (25 mM Tris-HClpH7.5) and passed five times through a microfluidizer (chilled on ice)at 120 psi (pounds per square inch) (such as Microfluidizer Model 1108,Microfluidic Co. Newton, Mass.) to produce a burst cell suspension. PMSF(1.0 mM) was added to the burst cell suspension. The cell suspension washomogenized using a polytron homogenizer (30 seconds at full speed) andthen centrifuged at 30,000×g for 30 minutes. The pellet from thiscentrifugation (P1) was suspended in detergent wash buffer (25 mMTris-HCl pH7.5, 1% Triton X, 1% deoxycholate, all components availablefrom Sigma) at a volume to weight ratio of 10:1, incubated 30 minutes atroom temperature, and re-centrifuged at 30,000×g for 30 minutes. Thepellet from this centrifugation (P2) was suspended in breaking buffer ata volume to weight ratio of 10:1 and re-centrifuged at 30,000×g for 30minutes. The pellet obtained (P3) was shown by SDS-PAGE to containPDerf1_(303c), while the supernatant fractions from the above-mentionedcentrifugations did not contain PDerf1_(303c).

The pellet P3 was solubilized by homogenization in 60 ml WIBSsolubilization buffer (8M urea, 25 mM Tris-HCl, pH 9.5, 100 mMβ-mercaptoethanol, all available from Sigma), incubated for 30 minutesat room temperature, and centrifuged at 30,000×g for 30 minutes. Thesupernatant from this centrifugation contained the majority of thePDerf1_(303c) protein.

The supernatant was diluted 1:2 (v/v) with Q-Sepharose load buffer (8Murea, 25 mM Tris-HCl, pH7.5); the pH of the diluted supernatant wasadjusted to pH 7.5 and loaded at a flow rate of 5 ml/min onto a 10 mL QSepharose column (available from Amersham-Pharmacia Biotech). The columnwas washed with 5 column volumes of Q Sepharose load buffer. Boundprotein was eluted with a linear gradient to 100% Q-Sepharose elutionbuffer (8M urea, 1.0 M NaCl, 25 mM Tris-HCl pH 7.5, all available fromSigma). Fractions containing recombinant Der f 1 protein PDerf1_(303c)were identified by SDS-PAGE.

Fractions collected from Q Sepharose that contained PDerf1_(303c) werepooled and volume adjusted so that the protein concentration was 1 to 3mg/ml. The pooled protein fractions were reduced by treatment with 6 mMDTT (dithiothreitol, available from Sigma) at room temperature for 30minutes. Following reduction, oxidized glutathione, 25 to 125 mM, wasadded to induce the formation of mixed disulfides of the cysteineresidues of PDerf1_(303c). Refolding was initiated by rapid dilution to0.5 to 1.0 M urea using 50 mM Tris, pH 9.5, with the addition of 5 to 25mM of either reduced glutathione or cysteine. This mixture was incubatedat 4° C. for 10 to 20 hours with slow mixing. The mixture was thendialyzed against either PBS, pH 7.5 or 50 mM Tris-HCl pH 7.5, thencentrifuged at 30,000×g for 30 minutes. The resulting supernatantcontained properly refolded PDerf1_(303c). Purified, refoldedPDerf1_(303c) from E. coli was subjected to N-terminal amino acidsequencing, using methods known in the art. The N-terminal sequenceobtained was MRPASIKTFE EFKKAFNKNY ATV-, represented herein as SEQ IDNO:59. This sequence is identical to that of the N-terminal sequence ofpro-Derf 1 (SEQ ID NO:4) with the addition of methionine; thus the E.coli expressed and refolded Der f 1 protein appears to be the expectedPDerf1_(303c).

Example 5

This Example demonstrates the ability of recombinant Pichia-expressedand E. coli-expressed Der f 1 proteins of the present invention to bindto IgE from a number of mite allergic sera and compares such binding tothat obtained using native purified Der f 1 proteins or mite extracts.

Two samples of native purified Der f 1 protein were used. The first,denoted herein as Heska native Derf1, was purified as described in U.S.patent application Ser. No. 09/292,225, ibid. The second, denotedChapman native Derf1, was purified in the laboratory of Martin Chapman(University of Virginia Health Sciences Center, Charlottesville, Va.) inthe manner described in Lombardero, et al, 1990, J Immunology 144,1353-1360. Recombinant Der f 1 proteins expressed by P. pastoristransformed with nucleic acid molecule nDerf1_(909b) or nDerf1_(669b),i.e., PDerf1_(303b) or PDerf1_(223b), respectively, were produced asdescribed in Examples 1 and 2. Note that although the protein producedusing nDerf1_(909b) is referred to as PDerf1_(303b), that protein isactually a mature form of Der f 1, as processed by P. pastoris; seeExample 2. Recombinant Der f 1 protein expressed by E. coli transformedwith nucleic acid molecule nDerf1_(909c), i.e., PDerf1_(303c), wasproduced as described in Example 4. Whole D. farinae and D.pteronyssinus mite extracts were prepared using techniques known tothose skilled in the art; see, for example, U.S. patent application Ser.No. 09/292,225, ibid.

Native or recombinant Der f 1 proteins in 100 μl CBC buffer (50 mMsodium carbonate, pH 9.6) were coated onto wells (100 ng per well) ofImmulon II microtiter plates (available from Dynex Technologies,Chantilly, Va.) by incubation at 4° C., covered, overnight. Excess fluidwas removed and wells were blocked with 200 μl Assay Buffer (4% fetalcalf serum (available from Summit Laboratories, Fort Collins, Colo.) inphosphate buffered saline (PBS, recipe in Sambrook, ibid.), plus 0.05%Tween-20 (available from Sigma, St. Louis, Mo.)) for one hour at roomtemperature. Plates were then washed for 4 cycles on an automatic platewasher (Ultrawash, available from Dynatech Laboratories) using PBS with0.05% Tween-20. The following serum samples, 100 μl per well, diluted1:20 in Assay Buffer, were incubated overnight at 4° C.: separate serumsamples collected from humans or dogs as indicated in Tables 1, 2 and 3;a pool of mite-allergic human sera; and a pool of mite-allergic dogsera. Control wells were treated identically except that no serum wasadded. Plates were then washed as described above. Biotinylated humanIgE receptor alpha chain (Fc_(ε)R1α-biotin) (100 μl of 1.3 ng/ml)prepared as described in U.S. Pat. No. 5,945,294, ibid., was added andincubated for one hour at room temperature. After this incubation,plates were washed as described above. Streptavidin-horseradishperoxidase conjugate (0.5 mg/ml, available from KPL Labs, Gaithersburg,Md.) was added at a 1:5000 dilution in Assay Buffer for one hour at roomtemperature, after which plates were washed as described above. TMBPeroxidase substrate system, 2 part (available from KPL Labs, #0-76-00),added at 100 μl per well, was used according to the manufacturer'sdirections. The color reaction was allowed to proceed until good colordevelopment was reached (about 10-15 min); then the reaction was stoppedwith 100 μl per well of 1 M phosphoric acid. Bound IgE was determined bymeasuring absorbance (Optical Density, or OD) at 450 nm (nanometers)using an ELISA plate reader (such as Spectramax”, Molecular Devices,Sunnyvale, Calif.). Background OD readings in the control wells weresubtracted from all numbers. Results are reported in Tables 1, 2 and 3as OD multiplied by 1000. OD numbers greater than 100 are considered tobe positive for a reaction with IgE. P. pastoris-expressed proteins aredenoted in the Tables as Pichia expressed proteins.

TABLE 1 Assay Number 1. Binding of IgE from mite-allergic human and dogsera to recombinant Pichia-expressed Derf1, to recombinant E.coli-expressed Derf1, to native purified Derf1 protein, or to whole D.farinae or D. pteronyssinus extracts. OD, OD, OD, OD, E. coli ChapmanHeska Pichia OD, Whole OD, expressed native native expressed D. farinaeWhole D. pteronyssinus Serum PDerf1_(303c) Derf1 Derf1 PDerf1_(303b)extract extract human 1916 18 17 51 11 25 66 human 3848 2291 2336 31231192 3871 4200 human 3958 147 1261 3368 2244 3411 4134 human 3960 14421024 2279 646 4048 4200 human 3961 67 326 1479 433 490 1130 human 39871416 1216 3741 1377 2836 3816 human 4289 29 287 777 182 1318 1746 human4467 236 615 1302 694 2527 2994 human 5207 1902 2669 3051 2153 3459 3933human pool 883 1531 1732 1547 3128 3499 dog pool 615 341 750 364 34873643 dog-1 0 6 3 21 6 7 dog-2 258 1408 2245 1490 2453 1876 dog-3 45 31252839 2499 2857 928

The data in Table 1 indicate that serum samples collected from 8mite-allergic humans and the pooled human sera sample bound to (i.e.,showed reactivity with) native Der f 1 proteins; all 9 samples were alsoreactive to recombinant P. pastoris-expressed PDerf_(303b) protein;i.e., the recombinant P. pastoris-expressed Der f 1 protein bound to100% of the samples that bound to native Der f 1 proteins. Additionally,of the 3 mite-allergic dog serum samples reactive to native Der f 1proteins, all 3 samples were also reactive (i.e., 100% reactivity) torecombinant P. pastoris-expressed PDerf_(303b). The results of thisassay indicate that the P. pastoris-expressed recombinant PDerf_(303b)has the same relative IgE binding activity compared to the native Der f1 protein, indicating that the soluble Pichia expressed molecule isfunctionally equivalent to the native molecule with respect to abilityto bind IgE specific for mite allergy.

Furthermore, the data in Table 1 indicate that of the 9 mite-allergichuman serum samples reactive to native Der f 1 proteins, 7 samples werealso reactive (i.e., 78% reactivity) to recombinant E. coli-expressedPDerf1_(303c) protein. In addition, the E. coli-expressed protein boundto 1 of 2 dog serum samples that bound to native Der f 1 proteins. Theseresults indicate that the pro-form of Der f 1 protein, expressed in E.coli and purified as described in Examples 3 and 4 has a biologicallyactive conformation that can bind to at least about 70% of serum samplesthat bind to native Der f 1 protein.

TABLE 2 Assay Number 2. Binding of IgE from mite-allergic or normalhuman and dog sera to recombinant Pichia-expressed Derf1, to recombinantE. coli-expressed Derf1, to native purified Derf1 protein, or to wholeD. farinae or D. pteronyssinus extracts. OD, OD, OD, OD, OD, E. coli-Chapman Heska Pichia- Whole OD, expressed native Native expressed D.farinae Whole D. pteronyssinus Serum PDerf1_(303c) Derf1 Derf1PDerf1_(303b) extract extract human 1916 21 8 62 15 43 62 human 38482378 1726 2362 904 3669 4200 human 3958 247 822 2235 2369 3052 4033human 3960 944 522 1308 1046 3386 3732 human 3961 46 169 784 709 5131109 human 3987 1477 846 2664 2457 2358 3673 human 4289 47 173 589 1601205 1665 human 4467 277 353 1051 660 2210 3011 human 5207 2122 21712746 1304 3215 3856 human pool 1161 1236 2599 1551 2886 3721 Heska humanB 0 0 0 2 24 45 Heska human C 4 0 0 4 5 5 Heska human D 0 0 0 0 0 0Heska human E 10 2 19 1 42 38 Heska human F 0 0 0 0 0 0 Heska human G 00 1 0 8 2 Heska human H 0 0 0 0 142 121 Heska human I 1 0 1 4 4 4 Heskahuman J 0 0 1 0 71 74 Heska human K 0 0 0 0 0 0 Heska human L 0 0 0 0 3532 Heska human M 0 0 51 0 448 573 Heska human N 24 373 885 370 521 763Heska human O 2 0 0 0 16 27 Heska human P 0 0 0 0 1 7 Heska human Q 0 00 0 1 7 Heska human R 0 0 1 0 94 58 dog sera pool A 489 220 449 199 31203521 146 dog sera pool 68 19 101 27 3665 4200 KS338

The results of Table 2 indicate that of the 10 human serum samples withIgE that bound to native Der f 1 proteins, IgE in all 10 samples alsobound to recombinant P. pastoris-expressed PDerf_(303b) protein; i.e.,the recombinant P. pastoris-expressed Der f 1 protein bound to 100% ofthe samples that bound to native Der f 1 proteins. Additionally, IgEfrom serum collected from a mite-allergic dog also bound to therecombinant P. pastoris-expressed Der f 1 protein. The results of thisassay indicate that the P. pastoris-expressed recombinant Der f1 proteinexpressed from nDerf1_(909b) has equivalent IgE binding activitycompared to the native Derf1.

Furthermore, the data in Table 2 indicate that of the 10 mite-allergichuman serum samples reactive to native Der f 1 proteins, 7 samples werealso reactive (i.e., 70% reactivity) to recombinant E. coli-expressedPDerf1_(303c) protein. In addition, the E. coli-expressed protein boundto the dog serum sample that bound to native Der f 1 proteins. Theseresults indicate that the pro-form of Der f 1 protein, expressed in E.coli and purified as described in Examples 3 and 4 has a biologicallyactive conformation that can bind to at least about 70% of serum samplesthat bind to native Der f 1 protein.

TABLE 3 Binding of IgE from mite-allergic human and dog sera torecombinant Pichia-expressed PDerf1_(303b), PDerf1_(223b), and topurified native mature Der f 1 protein. OD, Derf1, OD, Pichia-expressedOD, Pichia-expressed Chapman PDerf1_(303b), preparation PDerf1_(223b),Sera native number A166-26 prepararion 1000-7 1916 14 0 0 3848 1033 4571253 3958 1067 2616 1224 3960 738 1420 634 3961 221 744 301 3987 8652588 1078  429 152 104 63 4467 489 780 432 5207 1836 1887 1096 human1114 1226 774 pool

The data in Table 3 indicate that Der f 1 proteins expressed byrecombinant P. pastoris microorganisms transformed with nucleic acidmolecules encoding the pro-form or mature form of Der f 1 protein (i.e.,with nDerf1_(909b) or nDerf1_(669b), respectively), bind to IgE in serumfrom human patients with essentially the same reactivity as does nativeDer f 1 protein. As such, the soluble P. pastoris-expressed Der f 1proteins exhibit closely equivalent IgE binding activity as the nativeDer f 1 protein, indicating that they are expressed in a biologicallyactive conformation.

Example 6

This Example demonstrates the ability of recombinant P. pastoris and E.coli Der f 1 proteins of the present invention to bind to anti-Der f 1protein monoclonal antibodies.

Assays were carried out as follows. A microtiter plate as described inExample 5 was coated overnight at 4° C. with 100 ng/well of anti-Der f 1protein monoclonal antibody 6A8, denoted herein as anti-Der f 1 MAb 6A8,provided by Dr. Martin Chapman. The plate was washed in the mannerdescribed above. The following proteins were then added to wells, havingbeen diluted in Assay Buffer in a 2-fold dilution series, from 0.75 to50 ng/well: Heska native Derf1, P. pastoris-expressed PDerf1_(303b), andE. coli-expressed PDerf1_(303c). After incubation for 1 hour at roomtemperature, plates were washed as described in Example 5. Then 100 μlper well of a 1:1000 dilution in Assay Buffer of biotinylated anti-Der f1 monoclonal antibody 4C1, also denoted anti-Der f 1 MAb 4C1, providedby Dr. Martin Chapman, was added for 1 hour at room temperature. Plateswere washed, streptavidin-HRP conjugate was added, and plates weredeveloped as described in Example 5. Results are provided in Table 4.

TABLE 4 Monoclonal Capture ELISA. OD of native Der f 1 protein, Pichia-expressed Der f 1 protein, or E. coli-expressed Der f 1 protein capturedby anti-Der f 1 MAb 6A8 and detected by anti-Der f 1 MAb 4C1. ng proteinOD, OD, E. coli expressed OD, Pichia expressed per well native Derf1PDerf1_(303c) PDerf1_(303b) 50 2183 1983 2148 25 2142 1770 2156 2.5 22911372 2088 6.25 2197 890 1961 3.1 2219 503 1544 1.5 2043 268 916 0.751740 136 405

The results from Table 4 indicate that the binding activities of P.pastoris-expressed PDerf1_(303b) and E. coli expressed PDerf1_(303c), asmeasured in a monoclonal antibody capture assay with monoclonalantibodies 6A8 and 4C1, are similar to that of the native Der f 1protein.

Example 7

This Example demonstrates that a recombinant P. pastoris-expressedrecombinant Der f 1 protein of the present invention has cysteineprotease activity.

Native Der f 1 is believed to be a cysteine protease, based on homologyto papain; see, for example, Chua et al, 1992, J Exp Med 167, 175-182.The Der f 1 protein secreted as a mature form by recombinant cell P.pastoris HCY215 (i.e., P. pastoris strain X33 transformed with plasmidpBC128 containing nucleic acid molecule nDerf1_(909b) (coding strand ofSEQ ID NO:28) which encodes the pro-form of Der f 1 (amino acid sequenceSEQ ID NO:29)) was tested for cysteine protease activity in thefollowing manner. Three concentrations of protein were tested for theirabilities to cleave an artificial substrate in the presence or absenceof a cysteine protease inhibitor. Specifically, three pairs of samplescontaining 0.56 μg, 1.1 μg, or 5.6 μg of P. pastoris-expressed Der f 1protein, respectively, were incubated for 30 minutes at room temperaturein 20 μl of 50 mM Tris-HCl, pH 8. One member of each pair also containedthe irreversible cysteine protease inhibitor E-64 at a concentration of1 μg/ml. After the pre-incubation, 100 μl of 50 μM quenched fluorogenicsubstrate z-Val-Leu-Arg-AMC (available from Enzyme Systems Products,Livermore, Calif.) was added to all six samples, and the samples wereincubated for 2 hours at room temperature. Fluorescence was measuredusing a Perkin Elmer Luminescence Spectrometer (model #LS50B) at anexcitation wavelength of 380 nm and an emission wavelength of 460 nm.The results are shown in Table 5.

TABLE 5 Cysteine protease activity of P. pastoris-expressed Der f 1protein (rDer f 1) Micrograms % Inhibition by rDer f 1 Emission (w/oE-64) Emission (w/ E-64) E-64 5.6 9.671 2.369 76 1.1 1.693 0.765 55 0.560.861 0.302 65

These results indicate that the recombinant P. pastoris-expressed Der f1 protein exhibits cysteine protease activity that can be inhibited bypre-incubation with the cysteine protease inhibitor E-64. These results,combined with the IgE binding data of Examples 5 and 6, indicate thatrecombinant Der f 1 protein expressed by P. pastoris is secreted in abiologically active conformation.

Example 8

This Example demonstrates that a Der f 1 protein of the presentinvention lacking an N-glycosylation site selectively binds to IgE insera collected from mite allergic human patients in a manner similar toa Der f 1 protein having such a site.

A. The following Der f 1 proteins were reacted as described in Example 5with a pool of serum samples collected from 16 mite-allergic humanpatients: (a) Chapman native Der f 1, produced as described in Example5; (b) recombinant Der f 1 protein PDerf1_(303b), produced byrecombinant cell P. pastoris HCY215 (P. pastoris strain X33 transformedwith plasmid pBC128 containing nucleic acid molecule nDerf1_(909b)(coding strand of SEQ ID NO:28) which encodes the pro-form of Der f 1(amino acid sequence SEQ ID NO:29)), produced as described in Example1A; and (c) recombinant Der f 1 protein PDerf1_(303d), a Der f 1 proteinlacking an N-glycosylation site produced by recombinant cell P. pastorisHCY288 (P. pastoris strain X33 transformed with plasmid pBC158containing nucleic acid molecule nDerf1_(909d) (coding strand of SEQ IDNO:37) which encodes the pro-form of Der f 1 in which the asparagine atamino acid position 133 is replaced by glutamine (amino acid sequenceSEQ ID NO:38)), produced as described in Example 1A. Table 6 shows theresults of this assay, conducted at a variety of Der f 1 proteinconcentrations.

TABLE 6 Binding of IgE from pooled mite-allergic human sera torecombinant Pichia-expressed PDerf1_(303b), PDerf1_(303d), and topurified native mature Der f 1 protein. ng protein OD, native OD, Pichiaexpressed OD, Pichia expressed per well Der f 1 PDerf1_(303b)PDerf1_(303d) 200 584 484 1448 100 581 354 1097 50 488 293 779 25 215240 591 12.5 116 178 347 6.2 17 53 88

These results demonstrate that P. pastoris-expressed Der f 1 proteindoes not require an N-glycosylation site to selectively bind IgE inmite-allergic sera at least as well as native Der f 1 protein or P.pastoris-expressed Der f 1 protein with such a site. As such, it appearsthat N-linked glycosylation is not necessary for Der f 1 protein toreact with IgE from mite allergic sera.

B. The Der f 1 proteins described in Example 8B were reacted asdescribed in Example 6 with a pool of serum samples collected from 16mite-allergic human patients. Table 7 shows the results of this assay,conducted at a variety of Der f 1 protein concentrations.

TABLE 7 Monoclonal Capture ELISA. Binding of IgE from pooledmite-allergic human sera to recombinant Pichia-expressed PDerf1_(303b),PDerf1_(303d), and to purified native mature Der f 1 protein. ng proteinOD, native OD, Pichia expressed OD, Pichia expressed per well Der f 1PDerf1_(303b) PDerf1_(303d) 25 2249 2389 3007 12.5 2483 2388 3037 6.252620 2463 2991 3.1 2597 2103 2913 1.55 2447 1399 2626 0.78 2186 871 19630.39 1480 434 1380

These results further demonstrate that P. pastoris-expressed Der f 1protein does not require an N-glycosylation site to selectively bind IgEin mite-allergic sera at least as well as native Der f 1 protein or P.pastoris-expressed Der f 1 protein with such a site. As such, it appearsthat N-linked glycosylation is not necessary for Der f 1 protein toreact with IgE from mite allergic sera.

Example 9

This example describes the production of nucleic acid molecules encodingDer p 1 proteins for expression in E. coli.

A. Nucleic Acid Molecules Encoding the Pro Form of Der p1.

A three step PCR, using four oligonucleotides, was used to amplify a DNAfragment containing pro Der p 1 for cloning into expression plasmidpLambda Cro (produced as described in PCT Patent publication No.WO98/12563, hereinafter pLambdaCro). This process is analogous to thatdescribed for pro Der f 1 in Example 3, p. 63, to produce nDerf1_(909c).

Two separate PCR amplification reactions were performed: one usedforward and reverse primers EB160 with nucleic acid sequence5′-AGGAGACATATGCGTCCATCCTCGATCAAAACTTTTG, designated herein as SEQ IDNO:60, and EB163, with nucleic acid sequence5′-TTGTGCATTTGGACGACGGCATGATTGTTCTC, designated herein as SEQ ID NO:61,and 2×10⁷ plaque forming units (PFU) of a D. pteronyssinus cDNA libraryprepared from whole body mites in Lambda Zap (Stratagene, La Jolla,Calif.).

The other amplification reaction used forward and reverse primers EB161,with nucleic acid sequence 5′-TCACCCTGGATCCCTACAGGATGACAACGTATGGATATTC,designated herein as SEQ ID NO:62, and EB162, with nucleic acid sequence5′-GAGAACAATCATGCCGTCGTCCAAATGCACAA, designated herein as SEQ ID NO:63and 2×10⁷ PFU D. pteronyssinus cDNA library. Conditions for amplifyingand purifying the ˜0.6 and ˜0.4 kb fragments were as described inExample 3. The ˜0.6 and ˜0.4 kb fragments were annealed together andreamplified in vitro using primers EB160 and EB161, which incorporateNde1 (EB160) and BamH1 (EB161) restriction sites. The resulting 0.9 kbfragment was purified, digested with Nde1 and BamH1 and subcloned intosimilarly digested pLambdaCro to produce plasmid pBC194. The pro Der p 1coding sequence of pBC194 has 909 bases, and is designated herein as SEQID NO:64, and the reverse complement is designated as SEQ ID NO:66. Thecodon optimized arginine residues are encoded by positions 553 through558 of SEQ ID NO:64. The predicted amino acid sequence is SEQ ID NO:65.

B. Nucleic Acid Molecules Encoding the Mature Der p 1

The mature form of Derp1 was amplified from pBC194 DNA using Pfupolymerase and the following conditions: 1× manufacturers Pfu buffer,0.2 mM each dNTP, 0.4 uM each a) forward primer, KB20, with nucleic acidsequence 5′-AAAAAAAAACATATGACTAACGCCTGCAGTATCAATGGAAATG, designatedherein as SEQ ID NO:67, and b) reverse primer KB21, with nucleic acidsequence 5′-AAAAAAAAACTCGAGCTACAGGATGACAACGTATGGATATTC, designatedherein as SEQ ID NO:68, 26 ng pBC194, and 2.5 U Pfu polymerase, in a 50ul reaction volume. Amplification conditions were as follows: 1 cycle of95 C for 2 min, 30 cycles of [95 C for 1 min, 55 C for 1 min, 70 C for 1min], one cycle of 70 C for 10 min.

The resulting fragment was purified, digested with Nde1 and Xho 1, andsubcloned into similarly digested pLambdaCro to produce plasmid pBC204.The mature Der p 1 coding sequence of pBC204 has 669 bases, and isdesignated herein as SEQ ID NO:69, and the reverse complement isdesignated as SEQ ID NO:71. The predicted amino acid sequence is SEQ IDNO:70.

Example 10

This example describes the production of nucleic acid molecules encodingDer p1 proteins for expression in P. pichia.

A. Nucleic Acid Molecules Encoding Pro Der p 1

Four oligonucleotide primers were used to assemble an ˜900 bp fragmentcontaining a version of pro Der p 1 with selected arginine residuesoptimized for yeast codon bias. Primers EB132 and EB131 change arginineresidues specified by either CGA or CGT to AGA, the preferred codon inyeast (S. cerevisiae). Forward primer EB130, with nucleic acid sequence5′-GTGGCTCTCGAGAAGAGAGAGGCTCGTCCATCTTCCATCAAAACT, designated herein asSEQ ID NO:72, and reverse primer EB131, with nucleic acid sequence5′-CCGAATCTTTGTGCATTTGGTCTTCTGCATGATTGTTCTCGTGC, designated herein asSEQ ID NO:73, were used in combination with template DNA from a LambdaZap cDNA library and appropriate salts, enzymes, etc. (as described inExample 1, p. 56) to produce an ˜0.6 kb DNA fragment. Forward primerEB132, with nucleic acid sequence5′-GCACGAGAACAATCATGCAGAAGACCAAATGCACAAAGATTCGG, designated herein asSEQ ID NO:74, and reverse primer EB133, with nucleic acid sequence5′-GCTCTTGCGGCCGCTTACAAAATGACAACGTATGGATA, designated herein as SEQ IDNO:75, were used to amplify an approximately 0.4 kb DNA fragment. Theresulting 0.6 and 0.4 kb PCR fragments were annealed and reamplifiedusing primers EB130 and EB133 to produce an ˜0.9 kb DNA fragment thatwas subcloned as a Xho 1-Not 1 fragment into similarly digestedpPICZalpha B. The resulting plasmid was designated pBC169.

The Pro Der p 1 coding sequence of pBC169 has 906 bases, and isdesignated herein as SEQ ID NO:76, and the reverse complement isdesignated as SEQ ID NO:78. The predicted amino acid sequence isdesignated SEQ ID NO:77.

B. Nucleic Acid Molecules Encoding Mature Der p 1

An expression plasmid for secreting the mature form of Der p 1 fromPichia was constructed using forward primer EB154, with nucleic acidsequence 5′-GGGGTATCTCTCGAGAAGAGAACTAACGCCTGCAGTATCAATG, designatedherein as SEQ ID NO:79, and reverse primer EB155, with nucleic acidsequence 5′-AAGCTGGCGGCCGCTTACAAAATGACAACGTATGGATATTC, designated hereinas SEQ ID NO:80, and plasmid pBC169 as template DNA. Conditions foramplification and cloning were as described for the analogous plasmidfor expressing mature Der f 1 in Pichia (See Example 1B, p. 57-58). Theresulting molecule was digested with Xho 1 and Not 1, and inserted intosimilarly digested pPICZαA to form pBC185. The mature Der p 1 codingsequences of pBC185 has 666 nucleotides and is designated herein as SEQID NO:81, and the reverse complement is designated herein as SEQ IDNO:83. The expected protein product of mature Der p 1 has 222 aminoacids, and is designated herein as SEQ ID NO:82.

Example 11

This example describes the production of an N-Glycosylation site mutantof pro Der p 1 for expression in Pichia.

Residues 52 to 54 of mature Der p 1 (SEQ ID NO:82) contain a putativeN-linked glycosylation site: NQS. A cloning strategy analogous to onethe described for pro Der f 1 (N53Q) (Example 1C, p. 58) was used tomutate residue serine 54 (TCA) of the mature Der p 1 (SEQ ID NO:81) toglycine (GGT). Forward and reverse primers for mutagenic PCR were EB146,with nucleic acid sequence 5′-AAATAAGCTGATTCAGTTGCGGCAACACCAGAG,designated herein as SEQ ID NO:84, and EB147, with nucleic acid sequence(5′-GGCTTACCGTAATCAAGGTTTGGATCTTGCTG, designated herein as SEQ ID NO:85,respectively. The DNA template for mutagenic PCR was plasmid pBC169. Theamplified fragment was digested with Xho1 and Not1 and inserted intosimilarly digested pPICZαA. The plasmid with the mutated sequence (proDer p 1 S54G) was designated pBC175. The pro Der p1 S54G encodingsequence is 906 nucleotides and has the sequence designated herein asSEQ ID NO:86, and the reverse complement is designated as SEQ ID NO:88.The predicted amino acid sequence is SEQ ID NO:87, and has a glycine atresidue 54, rather than the serine present at that position in SEQ IDNO:82.

Example 12

This Example describes the production of a variant of a mite Group 1protein of the present invention in which the pro-peptide is expected tobe unable to self-process.

The in vitro protease activity of rDer f 1, combined with theobservation that Pichia strains engineered to produce pro-Der f 1secrete mature Der f 1, suggests that the pro-peptide undergoesself-processing.

A version of pro Der f 1 with a residue change at C35 of SEQ ID NO:32,the predicted active site cysteine, was produced (pBC182).

Plasmid pBC182 was constructed by mutagensis of plasmid pBC128 (pro Derf 1). Primers for inverse PCR were EB152, with nucleic acid sequence5′P-GCTGTGGTTCATCTTGGGCTTTCTCTGGTGTT, designated herein as SEQ ID NO:89,and EB153, with nucleic acid sequence5′P-CTCCTTGCATACGGATTGGAGTGACAGTTCGC, designated herein as SEQ ID NO:90.Template DNA was pBC128. Conditions for amplification and cloning wereas described in Example 1C (page 58). The amplified fragment wasdigested with Xho 1 and Not 1, and inserted into similarly digestedpPICZAlphaB to form pBC182. The pro Der f1 C35S coding sequence ofpBC182 has 909 nucleotides, and is designated herein as SEQ ID NO:91,and the reverse complement is designated as SEQ ID NO:93. The cys to serchange introduced by primer EB152 is at position 35 of the proteinsequence, which is designated herein as SEQ ID NO:92.

The resulting rDer f 1 is expected to be secreted from Pichia as thepro-enzyme form if the processing event is self-catalyzed. The analogousvariant of Der p 1 is made at position C34 of SEQ ID NO:82. In the aboveexample, the active site cysteine was changed to serine. In anotherembodiment of the invention, the coding sequences may be mutated tosubstitute either valine or alanine at that position.

Another possible residue to target is H171 of Der f 1 of SEQ ID NO:32and H170 of Der p 1 of SEQ ID NO:82. The Cys and His residues arepostulated to form an active site thiolate-imidazolium ion pair.Disruption of this pair could impair the proteolytic function of theprotein and the mutant is therefore expected to be impaired inself-processing. The histidines may be changed to another amino acid,preferably alanine.

While various embodiments of the present invention have been describedin detail, it is apparent that modifications and adaptations of thoseembodiments will occur to those skilled in the art. It is to beexpressly understood, however, that such modifications and adaptationsare within the scope of the present invention, as set forth in thefollowing claims.

1. A method to produce a recombinant protein comprising a recombinantmite Group 1 protein or a fragment thereof comprising the steps of: (a)culturing a methyltrophic yeast microorganism transformed with a nucleicacid molecule encoding said recombinant mite Group 1 protein orfragment; and (b) recovering said recombinant mite Group 1 protein orfragment from said methyltrophic yeast microorganism; wherein saidrecombinant mite Group 1 protein or fragment is selected from the groupconsisting of: Dermatophagoides farinae, Dermatophagoides pteronyssinus,and Euroglyphus maynei recombinant mite Group 1 proteins (Der f 1, Der p1 and Eur m 1) or a fragment thereof and has a function selected fromthe group consisting of: selectively binding IgE and causingproliferation of a T cell that proliferates in response to a native miteGroup 1 protein selected from the group consisting of Der f 1, Der p 1and Eur m 1 and said nucleic acid molecule consists of a nucleic acidsequence selected from the group consisting of: SEQ ID NO:1, SEQ IDNO:4, SEQ ID NO:7, SEQ ID NO:13, SEQ ID NO:16, SEQ ID NO:19, SEQ IDNO:22, SEQ ID NO:25, SEQ ID NO:28, SEQ ID NO:31, SEQ ID NO:34, SEQ IDNO:37, SEQ ID NO:40, SEQ ID NO:43, SEQ ID NO:64, SEQ ID NO:69, SEQ IDNO:76, SEQ ID NO:81, SEQ ID NO:86, and SEQ ID NO:91 or a fragmentthereof and wherein said nucleic acid molecule is optionally fused to asignal sequence.
 2. The method of claim 1, wherein said methyltrophicyeast microorganism is of a genus selected from the group consisting ofa Pichia microorganism, a Hansenula microorganism, a Torulopsismicroorganism, and a Candida microorganism.
 3. The method of claim 1,wherein said methyltrophic yeast microorganism is of a species selectedfrom the group consisting of Pichia pastoris, Pichia acaciae, Pichiaanomala, Pichia augusta, Pichia capsulata, Pichia fabianii, Pichiafarinosa, Pichia guilliermondii, Pichia methanolica, Pichia norvegensis,Pichia pinus, Pichia stipitis, and Hansenula polymorpha.
 4. The methodof claim 1, wherein said methyltrophic yeast microorganism is Pichiapastoris. 5.-6. (canceled)
 7. The method of claim 1, wherein saidnucleic acid molecule encodes a recombinant mite Group 1 proteinselected from the group consisting of a pro-form of a recombinant miteGroup 1 protein and a mature form of a recombinant mite Group 1 protein.8. The method of claim 1, wherein said nucleic acid molecule encodes arecombinant mite Group 1 protein fused to a S. cerevisiae alpha factorsignal sequence. 9.-11. (canceled)
 12. The method of claim 1, whereinsaid recombinant mite Group 1 protein is selected from the groupconsisting of: (a) a recombinant mite Group 1 protein consisting of anamino acid sequence selected from the group consisting of SEQ ID NO:2,SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:14, SEQ ID NO:17, SEQ ID NO:20, SEQID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32, SEQ ID NO:35, SEQ IDNO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:65, SEQ ID NO:70, SEQ IDNO:77, SEQ ID NO:82, SEQ ID NO:87, and SEQ ID NO:92; and (b) arecombinant mite Group 1 protein that is a fragment of any of saidproteins of (a), wherein said fragment has a function selected from thegroup consisting of selectively binding IgE and causing proliferation ofa T cell that proliferates in response to a native mite Group 1 protein.13. The method of claim 1, wherein said recombinant mite Group 1 proteinis selected from the group consisting of a pro-form of said recombinantmite Group 1 protein and a mature form of said recombinant mite Group 1protein.
 14. The method of claim 1, wherein said recombinant mite Group1 protein is secreted by said methyltrophic yeast microorganism.
 15. Themethod of claim 1, wherein said recombinant mite Group 1 protein bindsto IgE of at least about 70% of serum samples comprising IgE thatselectively bind to a native mite Group 1 protein. 16.-40. (canceled)41. A methyltrophic yeast microorganism comprising a nucleic acidmolecule encoding a mite Group 1 protein fragment thereof wherein saidnucleic acid molecule consists of a nucleic acid sequence selected fromthe group consisting of: SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:7, SEQ IDNO:13, SEQ ID NO:16, SEQ ID NO:19, SEQ ID NO:22, SEQ ID NO:25, SEQ IDNO:28, SEQ ID NO:31, SEQ ID NO:34, SEQ ID NO:37, SEQ ID NO:40, SEQ IDNO:43, SEQ ID NO:64, SEQ ID NO:69, SEQ ID NO:76, SEQ ID NO:81, SEQ IDNO:86, and SEQ ID NO:91 or a fragment thereof, said recombinant miteGroup 1 protein or fragment is selected from the group consisting of:Dermatophagoides farinae, Dermatophagoides pteronyssinus, andEuroglyphus maynei recombinant mite Group 1 proteins (Der f 1, Der p 1and Eur m 1) or a fragment thereof and has a function selected from thegroup consisting of: selectively binding IgE and causing proliferationof a T cell that proliferates in response to a native mite Group 1protein selected from the group consisting of Der f 1, Der p 1 and Eur m1, said nucleic acid molecule being operatively linked to atranscription control sequence and wherein said nucleic acid molecule isoptionally fused to a signal sequence.
 42. (canceled)
 43. Themethyltrophic yeast microorganism of claim 41, wherein said nucleic acidmolecule consists of a nucleic acid sequence selected from the groupconsisting of: SEQ ID NO:1, SEQ ID NO:4, SEQ ID NO:7, SEQ ID NO:13, SEQID NO:16, SEQ ID NO:19, SEQ ID NO:22, SEQ ID NO:25, SEQ ID NO:28, SEQ IDNO:31, SEQ ID NO:34, SEQ ID NO:37, SEQ ID NO:40, SEQ ID NO:43, SEQ IDNO:64, SEQ ID NO:69, SEQ ID NO:76, SEQ ID NO:81, SEQ ID NO:86, and SEQID NO:91.
 44. (canceled)
 45. The methyltrophic yeast microorganism ofclaim 41, wherein said recombinant mite Group 1 protein is selected fromthe group consisting of: (a) a recombinant mite Group 1 proteinconsisting of an amino acid sequence selected from the group consistingof: SEQ ID NO:2, SEQ ID NO:5, SEQ ID NO:8, SEQ ID NO:14, SEQ ID NO:17,SEQ ID NO:20, SEQ ID NO:23, SEQ ID NO:26, SEQ ID NO:29, SEQ ID NO:32,SEQ ID NO:35. SEQ ID NO:38, SEQ ID NO:41, SEQ ID NO:44, SEQ ID NO:65,SEQ ID NO:70, SEQ ID NO:77, SEQ ID NO:82, SEQ ID NO:87, and SEQ IDNO:92; and (b) a recombinant mite Group 1 protein that is a fragment ofany of said proteins of (a), wherein said fragment has a functionselected from the group consisting of selectively binding IgE andcausing proliferation of a T cell that proliferates in response to anative mite Group 1 protein.
 46. The methyltrophic yeast microorganismof claim 41, wherein said methyltrophic yeast microorganism is of agenus selected from the group consisting of a Pichia microorganism, aHansenula microorganism, a Torulopsis microorganism, and a Candidamicroorganism.
 47. The methyltrophic yeast microorganism of claim 46,wherein said Pichia microorganism is P. pastoris.
 48. The methyltrophicyeast microorganism of claim 47, wherein said nucleic acid moleculeencodes a recombinant mite Group 1 protein fused to a S. cerevisiaealpha factor signal sequence. 49.-56. (canceled)
 57. A method to producea recombinant protein comprising a recombinant mite Group 1 protein or afragment thereof, comprising the steps of: (a) culturing a methyltrophicyeast microorganism transformed with a nucleic acid molecule encodingsaid recombinant mite Group 1 protein or fragment; and (b) recoveringsaid recombinant mite Group 1 protein or fragment from saidmethyltrophic yeast microorganism; wherein said recombinant mite Group 1protein or fragment is selected from the group consisting of:Dermatophagoides farinae, Dermatophagoides pteronyssinus, andEuroglyphus maynei recombinant mite Group 1 proteins (Der f 1, Derp 1and Eur m 1) or a fragment thereof and has a function selected from thegroup consisting of: selectively binding IgE and causing proliferationof a T cell that proliferates in response to a native mite Group 1protein selected from the group consisting of Der f 1, Der p 1 and Eur m1 and said nucleic acid molecule hybridizes under stringent conditionswith a nucleic acid sequence selected from the group consisting of: SEQID NO:1, SEQ ID NO:4, SEQ ID NO:7, SEQ ID NO:13, SEQ ID NO:16, SEQ IDNO:19, SEQ ID NO:22, SEQ ID NO:25, SEQ ID NO:28, SEQ ID NO:31, SEQ IDNO:34, SEQ ID NO:37, SEQ ID NO:40, SEQ ID NO:43, SEQ ID NO:64, SEQ IDNO:69, SEQ ID NO:76, SEQ ID NO:81, SEQ ID NO:86, and SEQ ID NO:91 or afragment thereof and wherein said nucleic acid molecule is optionallyfused to a signal sequence.
 58. A method to produce a recombinantprotein comprising a recombinant mite Group 1 protein or a fragmentthereof, comprising the steps of: (a) culturing a methyltrophic yeastmicroorganism transformed with a nucleic acid molecule encoding saidrecombinant mite Group 1 protein or fragment; and (b) recovering saidrecombinant mite Group 1 protein or fragment from said methyltrophicyeast microorganism; wherein said recombinant mite Group 1 protein orfragment is selected from the group consisting of: Dermatophagoidesfarinae, Dermatophagoides pteronyssinus, and Euroglyphus mayneirecombinant mite Group 1 proteins (Der f 1, Der p 1 and Eur m 1) or afragment thereof and has a function selected from the group consistingof: selectively binding IgE and causing proliferation of a T cell thatproliferates in response to a native mite Group 1 protein selected fromthe group consisting of Der f 1, Der p 1 and Eur m 1 and said nucleicacid molecule having a sequence identity of at least 95% with a nucleicacid sequence selected from the group consisting of: SEQ ID NO: 1, SEQID NO:4, SEQ ID NO:7, SEQ ID NO:13, SEQ ID NO:16, SEQ ID NO:19, SEQ IDNO:22, SEQ ID NO:25, SEQ ID NO:28, SEQ ID NO:31, SEQ ID NO:34, SEQ IDNO:37, SEQ ID NO:40, SEQ ID NO:43, SEQ ID NO:64, SEQ ID NO:69, SEQ IDNO:76, SEQ ID NO:81, SEQ ID NO:86, and SEQ ID NO:91 or a fragmentthereof and wherein said nucleic acid molecule is optionally fused to asignal sequence.